diff --git a/changelog.txt b/changelog.txt
index 7ea3394574..f1f9fa2768 100644
--- a/changelog.txt
+++ b/changelog.txt
@@ -53,6 +53,7 @@
 * Update - Back button on the settings pages.
 * Update - Use individual product tax status instead of storewide tax setup when determining express checkout availability.
 * Add - Use Stripe Configuration API to manage payment methods enabled/disabled states.
+* Dev - Add track events when enabling/disabling payment methods.
 
 = 9.3.1 - 2025-03-14 =
 * Fix - Temporarily disables the subscriptions detached notice feature due to long loading times on stores with many subscriptions.
diff --git a/includes/admin/class-wc-rest-stripe-account-keys-controller.php b/includes/admin/class-wc-rest-stripe-account-keys-controller.php
index 7d23468cef..2a1be1bbea 100644
--- a/includes/admin/class-wc-rest-stripe-account-keys-controller.php
+++ b/includes/admin/class-wc-rest-stripe-account-keys-controller.php
@@ -299,7 +299,7 @@ public function set_account_keys( WP_REST_Request $request ) {
 				}
 			} else {
 				$upe_gateway = new WC_Stripe_UPE_Payment_Gateway();
-				$upe_gateway->update_option( 'upe_checkout_experience_accepted_payments', [ WC_Stripe_Payment_Methods::CARD, WC_Stripe_Payment_Methods::LINK ] );
+				$upe_gateway->update_enabled_payment_methods( [ WC_Stripe_Payment_Methods::CARD, WC_Stripe_Payment_Methods::LINK ] );
 
 				// Handle Multibanco separately as it is a non UPE method but it is part of the same settings page.
 				$multibanco = WC_Stripe_Helper::get_legacy_payment_method( 'stripe_multibanco' );
diff --git a/includes/admin/class-wc-rest-stripe-settings-controller.php b/includes/admin/class-wc-rest-stripe-settings-controller.php
index 20f74a470a..77a0d02a72 100644
--- a/includes/admin/class-wc-rest-stripe-settings-controller.php
+++ b/includes/admin/class-wc-rest-stripe-settings-controller.php
@@ -241,7 +241,7 @@ public function get_settings() {
 		$is_upe_enabled               = WC_Stripe_Feature_Flags::is_upe_checkout_enabled();
 		$available_payment_method_ids = $is_upe_enabled ? $this->gateway->get_upe_available_payment_methods() : WC_Stripe_Helper::get_legacy_available_payment_method_ids();
 		$ordered_payment_method_ids   = $is_upe_enabled ? WC_Stripe_Helper::get_upe_ordered_payment_method_ids( $this->gateway ) : $available_payment_method_ids;
-		$enabled_payment_method_ids   = $is_upe_enabled ? WC_Stripe_Helper::get_upe_settings_enabled_payment_method_ids( $this->gateway ) : WC_Stripe_Helper::get_legacy_enabled_payment_method_ids();
+		$enabled_payment_method_ids   = $is_upe_enabled ? $this->gateway->get_upe_enabled_payment_method_ids() : WC_Stripe_Helper::get_legacy_enabled_payment_method_ids();
 
 		return new WP_REST_Response(
 			[
@@ -604,6 +604,10 @@ private function update_enabled_payment_methods( WP_REST_Request $request ) {
 			return;
 		}
 
+		if ( null === $payment_method_ids_to_enable ) {
+			return;
+		}
+
 		if ( ! $is_upe_enabled ) {
 			$currently_enabled_payment_method_ids = WC_Stripe_Helper::get_legacy_enabled_payment_method_ids();
 			$payment_gateways                     = WC_Stripe_Helper::get_legacy_payment_methods();
@@ -620,26 +624,8 @@ private function update_enabled_payment_methods( WP_REST_Request $request ) {
 			return;
 		}
 
-		if ( null === $payment_method_ids_to_enable ) {
-			return;
-		}
-
-		$currently_enabled_payment_method_ids      = (array) $this->gateway->get_option( 'upe_checkout_experience_accepted_payments' );
-		$upe_checkout_experience_accepted_payments = [];
-
-		foreach ( WC_Stripe_UPE_Payment_Gateway::UPE_AVAILABLE_METHODS as $gateway ) {
-			if ( in_array( $gateway::STRIPE_ID, $payment_method_ids_to_enable, true ) ) {
-				$upe_checkout_experience_accepted_payments[] = $gateway::STRIPE_ID;
-			}
-		}
-
-		$this->gateway->update_option( 'upe_checkout_experience_accepted_payments', $upe_checkout_experience_accepted_payments );
-
-		// After updating payment methods record tracks events.
-		$newly_enabled_methods  = array_diff( $upe_checkout_experience_accepted_payments, $currently_enabled_payment_method_ids );
-		$newly_disabled_methods = array_diff( $currently_enabled_payment_method_ids, $payment_method_ids_to_enable );
-
-		$this->record_payment_method_settings_event( $newly_enabled_methods, $newly_disabled_methods );
+		$upe_gateway = new WC_Stripe_UPE_Payment_Gateway();
+		$upe_gateway->update_enabled_payment_methods( $payment_method_ids_to_enable );
 	}
 
 	/**
diff --git a/includes/admin/class-wc-stripe-payment-gateways-controller.php b/includes/admin/class-wc-stripe-payment-gateways-controller.php
index 6114587947..3ef6dc58ff 100644
--- a/includes/admin/class-wc-stripe-payment-gateways-controller.php
+++ b/includes/admin/class-wc-stripe-payment-gateways-controller.php
@@ -18,7 +18,8 @@ class WC_Stripe_Payment_Gateways_Controller {
 	public function __construct() {
 		// If UPE is enabled and there are enabled payment methods, we need to load the disable Stripe confirmation modal.
 		$stripe_settings              = WC_Stripe_Helper::get_stripe_settings();
-		$enabled_upe_payment_methods  = isset( $stripe_settings['upe_checkout_experience_accepted_payments'] ) ? $stripe_settings['upe_checkout_experience_accepted_payments'] : [];
+		$upe_gateway                  = new WC_Stripe_UPE_Payment_Gateway();
+		$enabled_upe_payment_methods  = $upe_gateway->get_upe_enabled_payment_method_ids();
 		$upe_payment_requests_enabled = 'yes' === $stripe_settings['payment_request'];
 
 		if ( ( is_array( $enabled_upe_payment_methods ) && count( $enabled_upe_payment_methods ) > 0 ) || $upe_payment_requests_enabled ) {
diff --git a/includes/admin/stripe-settings.php b/includes/admin/stripe-settings.php
index bd2a5e72f3..53062c0bcc 100644
--- a/includes/admin/stripe-settings.php
+++ b/includes/admin/stripe-settings.php
@@ -307,14 +307,6 @@
 			'desc_tip'    => true,
 		],
 	];
-	if ( WC_Stripe_Feature_Flags::is_upe_checkout_enabled() ) {
-		// This adds the payment method section
-		$upe_settings['upe_checkout_experience_accepted_payments'] = [
-			'title'   => __( 'Payments accepted on checkout (Early access)', 'woocommerce-gateway-stripe' ),
-			'type'    => 'upe_checkout_experience_accepted_payments',
-			'default' => [ WC_Stripe_Payment_Methods::CARD, WC_Stripe_Payment_Methods::LINK ],
-		];
-	}
 	// Insert UPE options below the 'logging' setting.
 	$stripe_settings = array_merge( $stripe_settings, $upe_settings );
 }
diff --git a/includes/class-wc-stripe-api.php b/includes/class-wc-stripe-api.php
index 743e75f04c..0ce455bb3d 100644
--- a/includes/class-wc-stripe-api.php
+++ b/includes/class-wc-stripe-api.php
@@ -23,6 +23,34 @@ class WC_Stripe_API {
 	 */
 	private static $secret_key = '';
 
+	/**
+	 * Instance of WC_Stripe_API.
+	 *
+	 * @var WC_Stripe_API
+	 */
+	private static $instance;
+
+	/**
+	 * Get instance of WC_Stripe_API.
+	 *
+	 * @return WC_Stripe_API
+	 */
+	public static function get_instance() {
+		if ( ! isset( self::$instance ) ) {
+			self::$instance = new self();
+		}
+		return self::$instance;
+	}
+
+	/**
+	 * Set instance of WC_Stripe_API.
+	 *
+	 * @param WC_Stripe_API $instance
+	 */
+	public static function set_instance( $instance ) {
+		self::$instance = $instance;
+	}
+
 	/**
 	 * Set secret API Key.
 	 *
@@ -441,7 +469,20 @@ public static function should_detach_payment_method_from_customer() {
 	 *
 	 * @return array The response from the API request.
 	 */
-	public static function get_payment_method_configurations() {
+	public function get_payment_method_configurations() {
 		return self::retrieve( 'payment_method_configurations' );
 	}
+
+	/**
+	 * Update the payment method configuration.
+	 *
+	 * @param array $payment_method_configurations The payment method configurations to update.
+	 */
+	public function update_payment_method_configurations( $id, $payment_method_configurations ) {
+		$response = self::request(
+			$payment_method_configurations,
+			'payment_method_configurations/' . $id
+		);
+		return $response;
+	}
 }
diff --git a/includes/class-wc-stripe-payment-method-configurations.php b/includes/class-wc-stripe-payment-method-configurations.php
new file mode 100644
index 0000000000..94027f6b32
--- /dev/null
+++ b/includes/class-wc-stripe-payment-method-configurations.php
@@ -0,0 +1,174 @@
+<?php
+
+if ( ! defined( 'ABSPATH' ) ) {
+	exit;
+}
+
+/**
+ * Class WC_Stripe_Payment_Method_Configurations
+ */
+class WC_Stripe_Payment_Method_Configurations {
+	/**
+	 * The primary configuration.
+	 *
+	 * @var object|null
+	*/
+	private static $primary_configuration = null;
+
+	/**
+	 * The test mode configuration parent ID.
+	 *
+	 * @var string|null
+	*/
+	const TEST_MODE_CONFIGURATION_PARENT_ID = 'pmc_1LEKjBGX8lmJQndTBOzjqxSa';
+
+	/**
+	 * The live mode configuration parent ID.
+	 *
+	 * @var string|null
+	*/
+	const LIVE_MODE_CONFIGURATION_PARENT_ID = 'pmc_1LEKjAGX8lmJQndTk2ziRchV';
+
+	/**
+	 * Reset the primary configuration.
+	 */
+	public static function reset_primary_configuration() {
+		self::$primary_configuration = null;
+	}
+
+	/**
+	 * Get the merchant payment method configuration in Stripe.
+	 *
+	 * @return object|null
+	*/
+	private static function get_primary_configuration() {
+		if ( null !== self::$primary_configuration ) {
+			return self::$primary_configuration;
+		}
+
+		$result = WC_Stripe_API::get_instance()->get_payment_method_configurations();
+		$payment_method_configurations = $result->data ?? null;
+
+		if ( ! $payment_method_configurations ) {
+			return null;
+		}
+
+		foreach ( $payment_method_configurations as $payment_method_configuration ) {
+			if ( ! $payment_method_configuration->livemode && $payment_method_configuration->parent && self::TEST_MODE_CONFIGURATION_PARENT_ID === $payment_method_configuration->parent ) {
+				self::$primary_configuration = $payment_method_configuration;
+				return $payment_method_configuration;
+			}
+
+			if ( $payment_method_configuration->livemode && $payment_method_configuration->parent && self::LIVE_MODE_CONFIGURATION_PARENT_ID === $payment_method_configuration->parent ) {
+				self::$primary_configuration = $payment_method_configuration;
+				return $payment_method_configuration;
+			}
+		}
+		return null;
+	}
+
+	/**
+	* Get the UPE enabled payment method IDs.
+	*
+	* @return array
+	*/
+	public static function get_upe_enabled_payment_method_ids() {
+		$enabled_payment_method_ids            = [];
+		$merchant_payment_method_configuration = self::get_primary_configuration();
+
+		if ( $merchant_payment_method_configuration ) {
+			foreach ( $merchant_payment_method_configuration as $payment_method_id => $payment_method ) {
+				if ( isset( $payment_method->display_preference->value ) && 'on' === $payment_method->display_preference->value ) {
+					$enabled_payment_method_ids[] = $payment_method_id;
+				}
+			}
+		}
+
+		return $enabled_payment_method_ids;
+	}
+
+	/**
+	 * Update the payment method configuration.
+	 *
+	 * @param array $enabled_payment_method_ids
+	 * @param array $available_payment_method_ids
+	*/
+	public static function update_payment_method_configuration( $enabled_payment_method_ids, $available_payment_method_ids ) {
+		$payment_method_configuration         = self::get_primary_configuration();
+		$updated_payment_method_configuration = [];
+		$newly_enabled_methods                = [];
+		$newly_disabled_methods               = [];
+
+		foreach ( $available_payment_method_ids as $stripe_id ) {
+			$will_enable = in_array( $stripe_id, $enabled_payment_method_ids, true );
+
+			if ( 'on' === ( $payment_method_configuration->$stripe_id->display_preference->value ?? null ) && ! $will_enable ) {
+				$newly_disabled_methods[] = $stripe_id;
+			}
+
+			if ( 'off' === ( $payment_method_configuration->$stripe_id->display_preference->value ?? null ) && $will_enable ) {
+				$newly_enabled_methods[] = $stripe_id;
+			}
+
+			$updated_payment_method_configuration[ $stripe_id ] = [
+				'display_preference' => [
+					'preference' => in_array( $stripe_id, $enabled_payment_method_ids, true ) ? 'on' : 'off',
+				],
+			];
+		}
+
+		if ( ! $payment_method_configuration ) {
+			WC_Stripe_Logger::log( 'No primary payment method configuration found while updating payment method configuration' );
+			return;
+		}
+
+		WC_Stripe_API::get_instance()->update_payment_method_configurations(
+			$payment_method_configuration->id,
+			$updated_payment_method_configuration
+		);
+
+		self::record_payment_method_settings_event( $newly_enabled_methods, $newly_disabled_methods );
+	}
+
+	/**
+	 * Record tracks events for each payment method that was enabled or disabled.
+	 *
+	 * @param array $enabled_methods An array of payment method ids that were enabled.
+	 * @param array $disabled_methods An array of payment method ids that were disabled.
+	 *
+	 * @return void
+	 */
+	private static function record_payment_method_settings_event( $enabled_methods, $disabled_methods ) {
+		if ( ! function_exists( 'wc_admin_record_tracks_event' ) ) {
+			return;
+		}
+
+		$is_test_mode = WC_Stripe_Mode::is_test();
+
+		// Track the events for both arrays.
+		array_map(
+			function ( $id ) use ( $is_test_mode ) {
+				wc_admin_record_tracks_event(
+					'wcstripe_payment_method_settings_enabled',
+					[
+						'is_test_mode'   => $is_test_mode,
+						'payment_method' => $id,
+					]
+				);
+			},
+			$enabled_methods
+		);
+		array_map(
+			function ( $id ) use ( $is_test_mode ) {
+				wc_admin_record_tracks_event(
+					'wcstripe_payment_method_settings_disabled',
+					[
+						'is_test_mode'   => $is_test_mode,
+						'payment_method' => $id,
+					]
+				);
+			},
+			$disabled_methods
+		);
+	}
+}
diff --git a/includes/connect/class-wc-stripe-connect.php b/includes/connect/class-wc-stripe-connect.php
index 43ad8b8da6..48353bed1f 100644
--- a/includes/connect/class-wc-stripe-connect.php
+++ b/includes/connect/class-wc-stripe-connect.php
@@ -240,8 +240,9 @@ private function get_default_stripe_config() {
 				}
 			}
 
-			$result['upe_checkout_experience_enabled']             = 'yes';
-			$result['upe_checkout_experience_accepted_payments'][] = WC_Stripe_Payment_Methods::LINK;
+			$result['upe_checkout_experience_enabled'] = 'yes';
+			$upe_gateway                               = new WC_Stripe_UPE_Payment_Gateway();
+			$upe_gateway->update_enabled_payment_methods( [ WC_Stripe_Payment_Methods::LINK ] );
 
 			return $result;
 		}
diff --git a/includes/payment-methods/class-wc-stripe-upe-payment-gateway.php b/includes/payment-methods/class-wc-stripe-upe-payment-gateway.php
index 6fbba581f7..738a062185 100644
--- a/includes/payment-methods/class-wc-stripe-upe-payment-gateway.php
+++ b/includes/payment-methods/class-wc-stripe-upe-payment-gateway.php
@@ -607,12 +607,12 @@ private function get_enabled_payment_method_config() {
 	}
 
 	/**
-	 * Returns the list of enabled payment method types for UPE.
+	 * Returns UPE enabled payment method IDs.
 	 *
 	 * @return string[]
 	 */
 	public function get_upe_enabled_payment_method_ids() {
-		return $this->get_option( 'upe_checkout_experience_accepted_payments', [ WC_Stripe_Payment_Methods::CARD ] );
+		return WC_Stripe_Payment_Method_Configurations::get_upe_enabled_payment_method_ids();
 	}
 
 	/**
@@ -664,6 +664,40 @@ public function get_upe_available_payment_methods() {
 		return $available_payment_methods;
 	}
 
+	/**
+	 * Updates the enabled payment methods.
+	 *
+	 * @param string[] $payment_method_ids_to_enable
+	 */
+	public function update_enabled_payment_methods( $payment_method_ids_to_enable ) {
+		WC_Stripe_Payment_Method_Configurations::update_payment_method_configuration( $payment_method_ids_to_enable, $this->get_stripe_supported_payment_methods() );
+	}
+
+	/**
+	 * Returns the list of supported payment method types for Stripe.
+	 *
+	 * @return string[]
+	 */
+	private function get_stripe_supported_payment_methods() {
+		$supported_stripe_ids         = [];
+		$available_payment_method_ids = $this->get_upe_available_payment_methods();
+
+		foreach ( self::UPE_AVAILABLE_METHODS as $gateway_class ) {
+			$gateway = new $gateway_class();
+
+			if (
+				! in_array( $gateway->get_id(), $available_payment_method_ids, true ) ||
+				( $gateway->get_supported_currencies() && ! in_array( get_woocommerce_currency(), $gateway->get_supported_currencies(), true ) )
+			) {
+				continue;
+			}
+
+			$supported_stripe_ids[] = $gateway::STRIPE_ID;
+		}
+
+		return $supported_stripe_ids;
+	}
+
 	/**
 	 * Renders the UPE input fields needed to get the user's payment information on the checkout page
 	 */
diff --git a/includes/payment-methods/class-wc-stripe-upe-payment-method-amazon-pay.php b/includes/payment-methods/class-wc-stripe-upe-payment-method-amazon-pay.php
index 7376a627fd..8d124d771d 100644
--- a/includes/payment-methods/class-wc-stripe-upe-payment-method-amazon-pay.php
+++ b/includes/payment-methods/class-wc-stripe-upe-payment-method-amazon-pay.php
@@ -73,7 +73,8 @@ public static function is_amazon_pay_enabled() {
 			return false;
 		}
 
-		$upe_enabled_method_ids = WC_Stripe_Helper::get_settings( null, 'upe_checkout_experience_accepted_payments' );
+		$wc_stripe_upe_payment_method_amazon_pay = new self();
+		$upe_enabled_method_ids = $wc_stripe_upe_payment_method_amazon_pay->get_upe_enabled_payment_method_ids();
 
 		return is_array( $upe_enabled_method_ids ) && in_array( self::STRIPE_ID, $upe_enabled_method_ids, true );
 	}
diff --git a/includes/payment-methods/class-wc-stripe-upe-payment-method-link.php b/includes/payment-methods/class-wc-stripe-upe-payment-method-link.php
index a733a0efb5..ec1092ebfb 100644
--- a/includes/payment-methods/class-wc-stripe-upe-payment-method-link.php
+++ b/includes/payment-methods/class-wc-stripe-upe-payment-method-link.php
@@ -39,7 +39,8 @@ public static function is_link_enabled() {
 			return false;
 		}
 
-		$upe_enabled_method_ids = WC_Stripe_Helper::get_settings( null, 'upe_checkout_experience_accepted_payments' );
+		$upe_gateway            = new WC_Stripe_UPE_Payment_Gateway();
+		$upe_enabled_method_ids = $upe_gateway->get_upe_enabled_payment_method_ids();
 
 		return is_array( $upe_enabled_method_ids ) && in_array( self::STRIPE_ID, $upe_enabled_method_ids, true );
 	}
diff --git a/includes/payment-methods/class-wc-stripe-upe-payment-method.php b/includes/payment-methods/class-wc-stripe-upe-payment-method.php
index 86963b0ff2..054703ed43 100644
--- a/includes/payment-methods/class-wc-stripe-upe-payment-method.php
+++ b/includes/payment-methods/class-wc-stripe-upe-payment-method.php
@@ -126,7 +126,7 @@ public function __construct() {
 		$main_settings     = WC_Stripe_Helper::get_stripe_settings();
 		$is_stripe_enabled = ! empty( $main_settings['enabled'] ) && 'yes' === $main_settings['enabled'];
 
-		$this->enabled                  = $is_stripe_enabled && in_array( static::STRIPE_ID, $this->get_option( 'upe_checkout_experience_accepted_payments', [ WC_Stripe_Payment_Methods::CARD ] ), true ) ? 'yes' : 'no'; // @phpstan-ignore-line (STRIPE_ID is defined in classes using this class)
+		$this->enabled                  = $is_stripe_enabled && in_array( static::STRIPE_ID, $this->get_upe_enabled_payment_method_ids(), true ) ? 'yes' : 'no'; // @phpstan-ignore-line (STRIPE_ID is defined in classes using this class)
 		$this->id                       = WC_Gateway_Stripe::ID . '_' . static::STRIPE_ID; // @phpstan-ignore-line (STRIPE_ID is defined in classes using this class)
 		$this->has_fields               = true;
 		$this->testmode                 = WC_Stripe_Mode::is_test();
@@ -758,4 +758,13 @@ public function get_transaction_url( $order ) {
 	public function supports_deferred_intent() {
 		return $this->supports_deferred_intent;
 	}
+
+	/**
+	 * Returns UPE enabled payment method IDs.
+	 *
+	 * @return string[]
+	 */
+	public function get_upe_enabled_payment_method_ids() {
+		return WC_Stripe_Payment_Method_Configurations::get_upe_enabled_payment_method_ids();
+	}
 }
diff --git a/package-lock.json b/package-lock.json
index 8a3c55ec6b..b3780cca32 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -6,7 +6,7 @@
   "packages": {
     "": {
       "name": "woocommerce-gateway-stripe",
-      "version": "9.2.0",
+      "version": "9.3.1",
       "hasInstallScript": true,
       "license": "GPL-3.0",
       "dependencies": {
diff --git a/readme.txt b/readme.txt
index cdc7612c0f..7db3ed0901 100644
--- a/readme.txt
+++ b/readme.txt
@@ -163,5 +163,6 @@ If you get stuck, you can ask for help in the [Plugin Forum](https://wordpress.o
 * Update - Back button on the settings pages.
 * Update - Use individual product tax status instead of storewide tax setup when determining express checkout availability.
 * Add - Use Stripe Configuration API to manage payment methods enabled/disabled states.
+* Dev - Add track events when enabling/disabling payment methods.
 
 [See changelog for all versions](https://raw.githubusercontent.com/woocommerce/woocommerce-gateway-stripe/trunk/changelog.txt).
diff --git a/tests/phpunit/admin/test-class-wc-rest-stripe-settings-controller-gb.php b/tests/phpunit/admin/test-class-wc-rest-stripe-settings-controller-gb.php
index ab027021ad..b9b15ed89a 100644
--- a/tests/phpunit/admin/test-class-wc-rest-stripe-settings-controller-gb.php
+++ b/tests/phpunit/admin/test-class-wc-rest-stripe-settings-controller-gb.php
@@ -9,7 +9,7 @@
 /**
  * WC_REST_Stripe_Settings_Controller_Test_GB unit tests.
  */
-class WC_REST_Stripe_Settings_Controller_Test_GB extends WP_UnitTestCase {
+class WC_REST_Stripe_Settings_Controller_Test_GB extends WC_Mock_Stripe_API_Unit_Test_Case {
 
 	/**
 	 * Tested REST route.
@@ -23,6 +23,13 @@ class WC_REST_Stripe_Settings_Controller_Test_GB extends WP_UnitTestCase {
 	 */
 	private static $gateway;
 
+	/**
+	 * Controller instance
+	 *
+	 * @var WC_REST_Stripe_Settings_Controller
+	 */
+	private $controller;
+
 	/**
 	 * Enable UPE and store gateway instance.
 	 *
@@ -82,6 +89,9 @@ public function set_up() {
 		$upe_helper = new UPE_Test_Helper();
 		$upe_helper->enable_upe();
 		$upe_helper->reload_payment_gateways();
+		$this->mock_payment_method_configurations( [ 'card' ], [] );
+
+		$this->controller = new WC_REST_Stripe_Settings_Controller( new WC_Stripe_UPE_Payment_Gateway() );
 
 		self::$gateway = WC()->payment_gateways()->payment_gateways()[ WC_Gateway_Stripe::ID ];
 	}
@@ -154,7 +164,7 @@ public function test_get_settings_returns_ordered_payment_method_ids_for_gb() {
 	private function rest_get_settings() {
 		$request = new WP_REST_Request( 'GET', self::SETTINGS_ROUTE );
 
-		return rest_do_request( $request );
+		return $this->controller->get_settings( $request );
 	}
 
 	/**
diff --git a/tests/phpunit/admin/test-class-wc-rest-stripe-settings-controller.php b/tests/phpunit/admin/test-class-wc-rest-stripe-settings-controller.php
index 76f8c7d698..dd1471c342 100644
--- a/tests/phpunit/admin/test-class-wc-rest-stripe-settings-controller.php
+++ b/tests/phpunit/admin/test-class-wc-rest-stripe-settings-controller.php
@@ -9,13 +9,21 @@
 /**
  * WC_REST_Stripe_Settings_Controller_Test unit tests.
  */
-class WC_REST_Stripe_Settings_Controller_Test extends WP_UnitTestCase {
+class WC_REST_Stripe_Settings_Controller_Test extends WC_Mock_Stripe_API_Unit_Test_Case {
 
 	/**
 	 * Tested REST route.
 	 */
 	const SETTINGS_ROUTE = '/wc/v3/wc_stripe/settings';
 
+	/**
+	 * Controller instance
+	 *
+	 * @var WC_REST_Stripe_Settings_Controller
+	 */
+	private $controller;
+
+
 	/**
 	 * Gateway instance that the controller uses.
 	 *
@@ -66,6 +74,9 @@ public function set_up() {
 			$this->markTestSkipped( 'The controller is not compatible with older WC versions, due to the missing `update_option` method on the gateway.' );
 		}
 
+		$this->upe_helper = new UPE_Test_Helper();
+		$this->controller = new WC_REST_Stripe_Settings_Controller( $this->get_gateway() );
+
 		add_action( 'rest_api_init', [ $this, 'deregister_wc_blocks_rest_api' ], 5 );
 
 		// Set the user so that we can pass the authentication.
@@ -80,6 +91,37 @@ public function tear_down() {
 		delete_option( WC_Stripe_Feature_Flags::AMAZON_PAY_FEATURE_FLAG_NAME );
 	}
 
+	/**
+	 * @dataProvider stripe_payment_method_configurations_provider
+	 */
+	public function test_get_stripe_payment_method_configurations_settings( $enabled_payment_method_ids, $disabled_payment_method_ids ) {
+		$this->mock_payment_method_configurations( $enabled_payment_method_ids, $disabled_payment_method_ids );
+
+		$response = $this->controller->get_settings();
+		$this->assertEquals( 200, $response->get_status() );
+		foreach ( $enabled_payment_method_ids as $payment_method ) {
+			$this->assertContains( $payment_method, $response->get_data()['enabled_payment_method_ids'] );
+		}
+		foreach ( $disabled_payment_method_ids as $payment_method ) {
+			$this->assertNotContains( $payment_method, $response->get_data()['enabled_payment_method_ids'] );
+		}
+	}
+
+	/**
+	 * Test that the update_settings method updates the payment method configurations settings.
+	 */
+	public function test_update_stripe_payment_method_configurations_settings() {
+		$this->mock_payment_method_configurations( [ 'card' ], [] );
+		$this->expect_payment_method_configurations_update( [ 'amazon_pay', 'card' ] );
+
+		$request = new WP_REST_Request( 'POST', self::SETTINGS_ROUTE );
+		$request->set_param( 'enabled_payment_method_ids', [ 'amazon_pay', 'card' ] );
+		$request->set_param( 'is_upe_enabled', true );
+
+		$response = $this->controller->update_settings( $request );
+		$this->assertEquals( 200, $response->get_status() );
+	}
+
 	/**
 	 * @dataProvider boolean_field_provider
 	 */
@@ -322,13 +364,15 @@ public function test_get_settings_returns_ordered_payment_method_ids() {
 	public function test_get_settings_fails_if_user_cannot_manage_woocommerce() {
 		$cb = $this->create_can_manage_woocommerce_cap_override( false );
 		add_filter( 'user_has_cap', $cb );
-		$response = $this->rest_get_settings();
+		$request  = new WP_REST_Request( 'GET', self::SETTINGS_ROUTE );
+		$response = rest_do_request( $request );
 		$this->assertEquals( 403, $response->get_status() );
 		remove_filter( 'user_has_cap', $cb );
 
 		$cb = $this->create_can_manage_woocommerce_cap_override( true );
 		add_filter( 'user_has_cap', $cb );
-		$response = $this->rest_get_settings();
+		$request  = new WP_REST_Request( 'GET', self::SETTINGS_ROUTE );
+		$response = rest_do_request( $request );
 		$this->assertEquals( 200, $response->get_status() );
 		remove_filter( 'user_has_cap', $cb );
 	}
@@ -375,16 +419,17 @@ public function boolean_field_provider() {
 		];
 	}
 
+	public function stripe_payment_method_configurations_provider() {
+		return [
+			'amazon_pay' => [ [ 'amazon_pay' ], [] ],
+			'amazon_pay' => [ [], [ 'amazon_pay' ] ],
+			'card'       => [ [ 'card', 'link' ], [] ],
+			'card'       => [ [], [ 'card', 'link' ] ],
+		];
+	}
+
 	public function enum_field_provider() {
 		return [
-			'enabled_payment_method_ids'       => [
-				'enabled_payment_method_ids',
-				'upe_checkout_experience_accepted_payments',
-				[ WC_Stripe_Payment_Methods::CARD ],
-				[ WC_Stripe_Payment_Methods::CARD, WC_Stripe_Payment_Methods::ALIPAY ],
-				[ 'foo' ],
-				true,
-			],
 			'payment_request_button_theme'     => [
 				'payment_request_button_theme',
 				'payment_request_button_theme',
@@ -454,7 +499,7 @@ public function deregister_wc_blocks_rest_api() {
 	private function rest_get_settings() {
 		$request = new WP_REST_Request( 'GET', self::SETTINGS_ROUTE );
 
-		return rest_do_request( $request );
+		return $this->controller->get_settings( $request );
 	}
 
 	/**
diff --git a/tests/phpunit/admin/test-wc-stripe-admin-notices.php b/tests/phpunit/admin/test-wc-stripe-admin-notices.php
index 759e3391c6..133bb36f05 100644
--- a/tests/phpunit/admin/test-wc-stripe-admin-notices.php
+++ b/tests/phpunit/admin/test-wc-stripe-admin-notices.php
@@ -1,6 +1,6 @@
 <?php
 
-class WC_Stripe_Admin_Notices_Test extends WP_UnitTestCase {
+class WC_Stripe_Admin_Notices_Test extends WC_Mock_Stripe_API_Unit_Test_Case {
 
 	public function set_up() {
 		parent::set_up();
@@ -95,17 +95,13 @@ function() {
 			]
 		);
 
-		$stripe_settings = array_merge(
-			WC_Stripe_Helper::get_stripe_settings(),
+		$this->mock_payment_method_configurations(
 			[
-				'upe_checkout_experience_accepted_payments' => [
-					WC_Stripe_Payment_Methods::GIROPAY,
-					WC_Stripe_Payment_Methods::BANCONTACT,
-					WC_Stripe_Payment_Methods::EPS,
-				],
+				WC_Stripe_Payment_Methods::GIROPAY,
+				WC_Stripe_Payment_Methods::BANCONTACT,
+				WC_Stripe_Payment_Methods::EPS,
 			]
 		);
-		WC_Stripe_Helper::update_main_stripe_settings( $stripe_settings );
 
 		update_option( 'wc_stripe_show_style_notice', 'no' );
 		update_option( 'home', 'https://...' );
diff --git a/tests/phpunit/bootstrap.php b/tests/phpunit/bootstrap.php
index 0fc6adf3c2..e6fd231361 100644
--- a/tests/phpunit/bootstrap.php
+++ b/tests/phpunit/bootstrap.php
@@ -51,6 +51,9 @@ function _manually_load_plugin() {
 
 require $_tests_dir . '/includes/bootstrap.php';
 
+# Load the WC Mock Stripe API Unit Test Case
+require_once __DIR__ . '/wc-mock-stripe-api-unit-test-case.php';
+
 # Load WooCommerce Helpers (https://github.com/woocommerce/woocommerce/tree/master/tests/legacy/framework/helpers)
 # To keep the plugin self-contained, copy any needed helper to the `helpers/` sub-folder.
 require_once __DIR__ . '/helpers/class-upe-test-helper.php';
diff --git a/tests/phpunit/helpers/class-upe-test-helper.php b/tests/phpunit/helpers/class-upe-test-helper.php
index 0d39ee74f8..1aa6d75c62 100644
--- a/tests/phpunit/helpers/class-upe-test-helper.php
+++ b/tests/phpunit/helpers/class-upe-test-helper.php
@@ -4,6 +4,16 @@
  * Provides methods useful when testing UPE-related logic.
  */
 class UPE_Test_Helper {
+	/**
+	 * Creates a mock object for the specified class
+	 *
+	 * @param string $class_name Name of the class to mock
+	 * @return PHPUnit\Framework\MockObject\MockObject
+	 */
+	private function create_mock( $class_name ) {
+		$mock_builder = new PHPUnit\Framework\MockObject\Generator();
+		return $mock_builder->getMock( $class_name );
+	}
 
 	public function enable_upe_feature_flag() {
 		// Force the UPE feature flag on.
diff --git a/tests/phpunit/helpers/class-wc-helper-stripe-api.php b/tests/phpunit/helpers/class-wc-helper-stripe-api.php
index 5cf9c14e02..689e6dac2f 100644
--- a/tests/phpunit/helpers/class-wc-helper-stripe-api.php
+++ b/tests/phpunit/helpers/class-wc-helper-stripe-api.php
@@ -11,7 +11,7 @@
  * This helper class should ONLY be used for unit tests!.
  * This helper class is used to mock static functions of WC_Stripe_API
  */
-class WC_Helper_Stripe_Api {
+class WC_Helper_Stripe_Api extends WC_Stripe_API {
 
 	/**
 	 * Retrieve response.
diff --git a/tests/phpunit/payment-methods/test-class-wc-stripe-upe-payment-gateway-gb.php b/tests/phpunit/payment-methods/test-class-wc-stripe-upe-payment-gateway-gb.php
index 64749c7abd..a69a37c7d0 100644
--- a/tests/phpunit/payment-methods/test-class-wc-stripe-upe-payment-gateway-gb.php
+++ b/tests/phpunit/payment-methods/test-class-wc-stripe-upe-payment-gateway-gb.php
@@ -2,7 +2,7 @@
 /**
  * Unit tests for the UPE payment gateway
  */
-class WC_Stripe_UPE_Payment_Gateway_Test_GB extends WP_UnitTestCase {
+class WC_Stripe_UPE_Payment_Gateway_Test_GB extends WC_Mock_Stripe_API_Unit_Test_Case {
 	/**
 	 * Initial setup.
 	 */
@@ -89,17 +89,4 @@ public function get_upe_available_payment_methods_provider() {
 			],
 		];
 	}
-
-	/**
-	 * @param array $account_data
-	 *
-	 * @return void
-	 */
-	private function set_stripe_account_data( $account_data ) {
-		WC_Stripe::get_instance()->account = $this->getMockBuilder( 'WC_Stripe_Account' )
-												->disableOriginalConstructor()
-												->setMethods( [ 'get_cached_account_data' ] )
-												->getMock();
-		WC_Stripe::get_instance()->account->method( 'get_cached_account_data' )->willReturn( $account_data );
-	}
 }
diff --git a/tests/phpunit/payment-methods/test-class-wc-stripe-upe-payment-gateway.php b/tests/phpunit/payment-methods/test-class-wc-stripe-upe-payment-gateway.php
index aadbaba01d..d02efd1e12 100644
--- a/tests/phpunit/payment-methods/test-class-wc-stripe-upe-payment-gateway.php
+++ b/tests/phpunit/payment-methods/test-class-wc-stripe-upe-payment-gateway.php
@@ -5,7 +5,7 @@
 /**
  * Unit tests for the UPE payment gateway
  */
-class WC_Stripe_UPE_Payment_Gateway_Test extends WP_UnitTestCase {
+class WC_Stripe_UPE_Payment_Gateway_Test extends WC_Mock_Stripe_API_Unit_Test_Case {
 	/**
 	 * Mock UPE Gateway
 	 *
@@ -21,11 +21,11 @@ class WC_Stripe_UPE_Payment_Gateway_Test extends WP_UnitTestCase {
 	private $mock_stripe_customer;
 
 	/**
-	 * Array mapping Stripe IDs to mock WC_Stripe_UPE_Payment_Methods.
+	 * Array of available payment methods.
 	 *
 	 * @var array
 	 */
-	private $mock_payment_methods;
+	private $available_payment_methods;
 
 	/**
 	 * Mocked value of return_url.
@@ -262,13 +262,7 @@ public function test_get_upe_enabled_at_checkout_payment_method_ids() {
 			WC_Stripe_UPE_Payment_Method_CC::STRIPE_ID,
 			WC_Stripe_UPE_Payment_Method_Link::STRIPE_ID,
 		];
-		$this->mock_gateway->update_option(
-			'upe_checkout_experience_accepted_payments',
-			[
-				WC_Stripe_Payment_Methods::CARD,
-				WC_Stripe_Payment_Methods::LINK,
-			]
-		);
+		$this->mock_payment_method_configurations( $available_payment_methods );
 		$this->assertSame( $available_payment_methods, $this->mock_gateway->get_upe_enabled_at_checkout_payment_method_ids() );
 	}
 
@@ -2276,6 +2270,8 @@ public function test_process_payment_deferred_intent_with_existing_intent() {
 		$currency    = $order->get_currency();
 		$order_id    = $order->get_id();
 
+		list( $amount ) = $this->get_order_details( $order );
+
 		$mock_intent = (object) wp_parse_args(
 			[
 				'payment_method'       => 'pm_mock',
@@ -2290,6 +2286,7 @@ public function test_process_payment_deferred_intent_with_existing_intent() {
 					],
 				],
 				'status'               => WC_Stripe_Intent_Status::REQUIRES_ACTION,
+				'amount'               => $amount,
 			],
 			self::MOCK_CARD_PAYMENT_INTENT_TEMPLATE
 		);
@@ -2425,6 +2422,7 @@ public function test_process_payment_creates_new_intent_when_existing_intent_fai
 		$order_id    = $order->get_id();
 
 		$mock_payment_method = (object) self::MOCK_CARD_PAYMENT_METHOD_TEMPLATE;
+		list( $amount )      = $this->get_order_details( $order );
 
 		// Create a mock failed payment intent that would be attached to the order
 		$mock_failed_intent = (object) wp_parse_args(
@@ -2436,6 +2434,7 @@ public function test_process_payment_creates_new_intent_when_existing_intent_fai
 				'charges'              => (object) [
 					'data' => [],
 				],
+				'amount'               => $amount,
 			],
 			self::MOCK_CARD_PAYMENT_INTENT_TEMPLATE
 		);
@@ -2653,19 +2652,6 @@ public function provide_test_filter_saved_payment_methods_list() {
 		];
 	}
 
-	/**
-	 * @param array $account_data
-	 *
-	 * @return void
-	 */
-	private function set_stripe_account_data( $account_data ) {
-		WC_Stripe::get_instance()->account = $this->getMockBuilder( 'WC_Stripe_Account' )
-												->disableOriginalConstructor()
-												->setMethods( [ 'get_cached_account_data' ] )
-												->getMock();
-		WC_Stripe::get_instance()->account->method( 'get_cached_account_data' )->willReturn( $account_data );
-	}
-
 	/**
 	 * Test test_set_payment_method_title_for_order.
 	 *
diff --git a/tests/phpunit/payment-methods/test-class-wc-stripe-upe-payment-method.php b/tests/phpunit/payment-methods/test-class-wc-stripe-upe-payment-method.php
index 66cf6d2064..6a652e7484 100644
--- a/tests/phpunit/payment-methods/test-class-wc-stripe-upe-payment-method.php
+++ b/tests/phpunit/payment-methods/test-class-wc-stripe-upe-payment-method.php
@@ -2,7 +2,7 @@
 /**
  * Unit tests for UPE payment methods
  */
-class WC_Stripe_UPE_Payment_Method_Test extends WP_UnitTestCase {
+class WC_Stripe_UPE_Payment_Method_Test extends WC_Mock_Stripe_API_Unit_Test_Case {
 	/**
 	 * Array of mocked UPE payment methods.
 	 *
@@ -936,46 +936,30 @@ public function test_update_payment_token() {
 	}
 
 	/**
-	 * Tests that UPE methods are only enabled if Stripe is enabled and the individual methods is enabled in the settings.
+	 * Tests that UPE methods are only enabled if Stripe is enabled.
 	 */
 	public function test_upe_method_enabled() {
-		// Enable Stripe and reset the accepted payment methods.
 		$stripe_settings            = WC_Stripe_Helper::get_stripe_settings();
 		$stripe_settings['enabled'] = 'yes';
-		$stripe_settings['upe_checkout_experience_accepted_payments'] = [];
 		WC_Stripe_Helper::update_main_stripe_settings( $stripe_settings );
 
-		// For each method we'll test the following combinations:
-		$stripe_enabled_settings    = [ 'yes', 'no', '' ];
-		$upe_method_enabled_options = [ true, false ];
+		$this->mock_payment_method_configurations( [ WC_Stripe_Payment_Methods::LINK ], [] );
 
-		foreach ( WC_Stripe_UPE_Payment_Gateway::UPE_AVAILABLE_METHODS as $payment_method ) {
-			foreach ( $stripe_enabled_settings as $stripe_enabled ) {
-				foreach ( $upe_method_enabled_options as $upe_method_enabled_option ) {
-					// Update the settings.
-					$stripe_settings['enabled'] = $stripe_enabled;
-
-					$payment_method_index = array_search( $payment_method::STRIPE_ID, $stripe_settings['upe_checkout_experience_accepted_payments'] );
-
-					if ( $upe_method_enabled_option && false === $payment_method_index ) {
-						$stripe_settings['upe_checkout_experience_accepted_payments'][] = $payment_method::STRIPE_ID;
-					} elseif ( ! $upe_method_enabled_option && false !== $payment_method_index ) {
-						unset( $stripe_settings['upe_checkout_experience_accepted_payments'][ $payment_method_index ] );
-					}
+		$link_upe_method = new WC_Stripe_UPE_Payment_Method_Link();
+		$this->assertTrue( $link_upe_method->is_enabled() );
+	}
 
-					WC_Stripe_Helper::update_main_stripe_settings( $stripe_settings );
+	/**
+	 * Tests that UPE methods are not enabled if Stripe is disabled.
+	 */
+	public function test_upe_method_disabled() {
+		$stripe_settings            = WC_Stripe_Helper::get_stripe_settings();
+		$stripe_settings['enabled'] = 'no';
+		WC_Stripe_Helper::update_main_stripe_settings( $stripe_settings );
 
-					// Verify that the payment method is enabled/disabled.
-					$payment_method_instance = new $payment_method();
+		$this->mock_payment_method_configurations( [ WC_Stripe_Payment_Methods::LINK ], [] );
 
-					// The UPE method is only enabled if Stripe is enabled and the method is enabled in the settings.
-					if ( 'yes' === $stripe_enabled && $upe_method_enabled_option ) {
-						$this->assertTrue( $payment_method_instance->is_enabled() );
-					} else {
-						$this->assertFalse( $payment_method_instance->is_enabled() );
-					}
-				}
-			}
-		}
+		$link_upe_method = new WC_Stripe_UPE_Payment_Method_Link();
+		$this->assertFalse( $link_upe_method->is_enabled() );
 	}
 }
diff --git a/tests/phpunit/payment-methods/test-wc-stripe-payment-request.php b/tests/phpunit/payment-methods/test-wc-stripe-payment-request.php
index 0f5fdf1297..914ccd4854 100644
--- a/tests/phpunit/payment-methods/test-wc-stripe-payment-request.php
+++ b/tests/phpunit/payment-methods/test-wc-stripe-payment-request.php
@@ -8,7 +8,7 @@
 /**
  * WC_Stripe_Payment_Request_Test class.
  */
-class WC_Stripe_Payment_Request_Test extends WP_UnitTestCase {
+class WC_Stripe_Payment_Request_Test extends WC_Mock_Stripe_API_Unit_Test_Case {
 	const SHIPPING_ADDRESS = [
 		'country'   => 'US',
 		'state'     => 'CA',
@@ -193,15 +193,7 @@ public function test_is_at_least_one_payment_request_button_enabled_link_enabled
 		$this->pr->stripe_settings = [ 'payment_request' => false ];
 
 		$this->upe_helper->enable_upe();
-
-		WC_Stripe_Helper::update_main_stripe_settings(
-			array_merge(
-				WC_Stripe_Helper::get_stripe_settings(),
-				[
-					'upe_checkout_experience_accepted_payments' => [ 'link' ],
-				]
-			)
-		);
+		$this->mock_payment_method_configurations( [ WC_Stripe_Payment_Methods::LINK ], [] );
 
 		$this->assertTrue( $this->pr->is_at_least_one_payment_request_button_enabled() );
 	}
@@ -216,15 +208,7 @@ public function test_is_at_least_one_payment_request_button_enabled_none_enabled
 		// Disable Apple Pay/Google Pay
 		$this->pr->stripe_settings = [ 'payment_request' => false ];
 
-		// Disable Link by Stripe
-		WC_Stripe_Helper::update_main_stripe_settings(
-			array_merge(
-				WC_Stripe_Helper::get_stripe_settings(),
-				[
-					'upe_checkout_experience_accepted_payments' => [ WC_Stripe_Payment_Methods::CARD ],
-				]
-			)
-		);
+		$this->mock_payment_method_configurations( [ WC_Stripe_Payment_Methods::CARD ], [] );
 
 		$this->assertFalse( $this->pr->is_at_least_one_payment_request_button_enabled() );
 	}
diff --git a/tests/phpunit/test-class-wc-stripe-notes.php b/tests/phpunit/test-class-wc-stripe-notes.php
index cfbcfd33b1..75286dbcde 100644
--- a/tests/phpunit/test-class-wc-stripe-notes.php
+++ b/tests/phpunit/test-class-wc-stripe-notes.php
@@ -8,9 +8,7 @@
 /**
  * Class WC_Stripe_Inbox_Notes_Note tests.
  */
-class WC_Stripe_Inbox_Notes_Test extends WP_UnitTestCase {
-	//  public static $global_woocommerce_gateway_stripe;
-
+class WC_Stripe_Inbox_Notes_Test extends WC_Mock_Stripe_API_Unit_Test_Case {
 	public $stripe_connect_mock;
 	public $stripe_connect_original;
 
@@ -24,6 +22,9 @@ public function set_up() {
 		$this->stripe_connect_original        = woocommerce_gateway_stripe()->connect;
 		woocommerce_gateway_stripe()->connect = $this->stripe_connect_mock;
 
+		$this->stripe_api = $this->createMock( WC_Stripe_API::class );
+		WC_Stripe_API::set_instance( $this->stripe_api );
+
 		if ( version_compare( WC_VERSION, '4.4.0', '<' ) ) {
 			$this->markTestSkipped( 'The used WC components are not backward compatible' );
 			return;
@@ -47,28 +48,25 @@ public function tear_down() {
 	}
 
 	public function test_create_upe_availability_note() {
-
+		WC_Stripe_Helper::update_main_stripe_settings( [ 'enabled' => 'yes' ] );
 		WC_Stripe_Inbox_Notes::create_upe_notes();
 		$admin_note_store = WC_Data_Store::load( 'admin-note' );
 		$this->assertSame( 1, count( $admin_note_store->get_notes_with_name( WC_Stripe_UPE_Availability_Note::NOTE_NAME ) ) );
 	}
 
 	public function test_create_upe_stripelink_note() {
+		$upe_helper = new UPE_Test_Helper();
+		$upe_helper->enable_upe();
+		$upe_helper->reload_payment_gateways();
+
 		WC_Stripe_Helper::update_main_stripe_settings(
 			[
 				'enabled'                         => 'yes',
 				'upe_checkout_experience_enabled' => 'yes',
 			]
 		);
-		WC_Stripe::get_instance()->account = $this->getMockBuilder( 'WC_Stripe_Account' )
-			->disableOriginalConstructor()
-			->setMethods(
-				[
-					'get_cached_account_data',
-				]
-			)
-			->getMock();
-		WC_Stripe::get_instance()->account->method( 'get_cached_account_data' )->willReturn( [ 'country' => 'US' ] );
+		$this->mock_payment_method_configurations( [ WC_Stripe_Payment_Methods::LINK, WC_Stripe_Payment_Methods::CARD ] );
+		$this->set_stripe_account_data( [ 'country' => 'US' ] );
 		WC_Stripe_Inbox_Notes::create_upe_notes();
 		$admin_note_store = WC_Data_Store::load( 'admin-note' );
 		$this->assertSame( 1, count( $admin_note_store->get_notes_with_name( WC_Stripe_UPE_StripeLink_Note::NOTE_NAME ) ) );
@@ -84,21 +82,19 @@ public function test_create_upe_notes_does_not_create_note_when_upe_preview_is_d
 	}
 
 	public function test_create_upe_notes_does_not_create_availability_note_when_upe_is_enbled() {
+		$upe_helper = new UPE_Test_Helper();
+		$upe_helper->enable_upe();
+		$upe_helper->reload_payment_gateways();
+
 		WC_Stripe_Helper::update_main_stripe_settings(
 			[
 				'enabled'                         => 'yes',
 				'upe_checkout_experience_enabled' => 'yes',
 			]
 		);
-		WC_Stripe::get_instance()->account = $this->getMockBuilder( 'WC_Stripe_Account' )
-			->disableOriginalConstructor()
-			->setMethods(
-				[
-					'get_cached_account_data',
-				]
-			)
-			->getMock();
-		WC_Stripe::get_instance()->account->method( 'get_cached_account_data' )->willReturn( [ 'country' => 'US' ] );
+
+		$this->set_stripe_account_data( [ 'country' => 'US' ] );
+		$this->mock_payment_method_configurations( [ WC_Stripe_Payment_Methods::LINK, WC_Stripe_Payment_Methods::CARD ] );
 		WC_Stripe_Inbox_Notes::create_upe_notes();
 
 		$admin_note_store = WC_Data_Store::load( 'admin-note' );
@@ -144,7 +140,7 @@ public function test_create_stripelink_note_unavailable_if_cc_not_enabled() {
 			]
 		);
 
-		$this->set_enabled_payment_methods( [ 'test' ] );
+		$this->mock_payment_method_configurations( [ 'test' ] );
 		WC_Stripe_Inbox_Notes::create_upe_notes();
 
 		$admin_note_store = WC_Data_Store::load( 'admin-note' );
@@ -160,30 +156,11 @@ public function test_create_stripelink_note_unavailable_link_enabled() {
 			]
 		);
 
-		$this->set_enabled_payment_methods( [ WC_Stripe_Payment_Methods::CARD, WC_Stripe_Payment_Methods::LINK ] );
+		$this->mock_payment_method_configurations( [ WC_Stripe_Payment_Methods::CARD, WC_Stripe_Payment_Methods::LINK ] );
 
-		WC_Stripe_Helper::update_main_stripe_settings(
-			array_merge(
-				WC_Stripe_Helper::get_stripe_settings(),
-				[
-					'upe_checkout_experience_accepted_payments' => [ WC_Stripe_Payment_Methods::CARD, WC_Stripe_Payment_Methods::LINK ],
-				]
-			)
-		);
 		WC_Stripe_Inbox_Notes::create_upe_notes();
 
 		$admin_note_store = WC_Data_Store::load( 'admin-note' );
 		$this->assertSame( 0, count( $admin_note_store->get_notes_with_name( WC_Stripe_UPE_StripeLink_Note::NOTE_NAME ) ) );
 	}
-
-	private function set_enabled_payment_methods( $payment_methods ) {
-		WC_Stripe_Helper::update_main_stripe_settings(
-			array_merge(
-				WC_Stripe_Helper::get_stripe_settings(),
-				[
-					'upe_checkout_experience_accepted_payments' => $payment_methods,
-				]
-			)
-		);
-	}
 }
diff --git a/tests/phpunit/test-wc-rest-stripe-account-keys-controller.php b/tests/phpunit/test-wc-rest-stripe-account-keys-controller.php
index a3aa4b42f2..9c72f0f33d 100644
--- a/tests/phpunit/test-wc-rest-stripe-account-keys-controller.php
+++ b/tests/phpunit/test-wc-rest-stripe-account-keys-controller.php
@@ -8,7 +8,7 @@
 /**
  * WC_REST_Stripe_Account_Keys_Controller unit tests.
  */
-class WC_REST_Stripe_Account_Keys_Controller_Test extends WP_UnitTestCase {
+class WC_REST_Stripe_Account_Keys_Controller_Test extends WC_Mock_Stripe_API_Unit_Test_Case {
 	/**
 	 * Tested REST route.
 	 */
@@ -162,16 +162,11 @@ public function test_changing_keys_resets_payment_methods() {
 		$request->set_param( 'publishable_key', '' );
 
 		// Set initial payment methods
-		$upe_gateway = new WC_Stripe_UPE_Payment_Gateway();
-		$upe_gateway->update_option( 'upe_checkout_experience_accepted_payments', [ WC_Stripe_Payment_Methods::CARD, WC_Stripe_Payment_Methods::LINK, WC_Stripe_Payment_Methods::SEPA, WC_Stripe_Payment_Methods::IDEAL ] );
+		$this->set_stripe_account_data( [ 'country' => 'US' ] );
+		$this->mock_payment_method_configurations( [ WC_Stripe_Payment_Methods::CARD, WC_Stripe_Payment_Methods::LINK, WC_Stripe_Payment_Methods::SEPA, WC_Stripe_Payment_Methods::IDEAL ], [] );
+		$this->expect_payment_method_configurations_update( [ WC_Stripe_Payment_Methods::CARD, WC_Stripe_Payment_Methods::LINK ] );
 
 		$this->controller->set_account_keys( $request );
-
-		// Retrieve the current enabled payment methods
-		$upe_gateway     = new WC_Stripe_UPE_Payment_Gateway();
-		$enabled_methods = count( $upe_gateway->get_option( 'upe_checkout_experience_accepted_payments' ) );
-
-		$this->assertEquals( 2, $enabled_methods ); // card and link are default payments
 	}
 
 	/**
diff --git a/tests/phpunit/test-wc-stripe.php b/tests/phpunit/test-wc-stripe.php
index ee588df624..8cb0449dab 100644
--- a/tests/phpunit/test-wc-stripe.php
+++ b/tests/phpunit/test-wc-stripe.php
@@ -1,6 +1,6 @@
 <?php
 
-class WC_Stripe_Test extends WP_UnitTestCase {
+class WC_Stripe_Test extends WC_Mock_Stripe_API_Unit_Test_Case {
 
 	/**
 	 * @var UPE_Test_Helper
@@ -10,6 +10,7 @@ class WC_Stripe_Test extends WP_UnitTestCase {
 	public function set_up() {
 		parent::set_up();
 		$this->upe_helper = new UPE_Test_Helper();
+		$this->set_stripe_account_data( [ 'country' => 'US' ] );
 	}
 
 	public function test_constants_defined() {
@@ -142,6 +143,8 @@ public function test_turning_on_upe_with_no_stripe_legacy_payment_methods_enable
 		$stripe_settings = WC_Stripe_Helper::get_stripe_settings();
 		$this->assertEquals( 'no', $stripe_settings['enabled'] );
 		$this->assertEquals( 'no', $stripe_settings['upe_checkout_experience_enabled'] );
+		$this->mock_payment_method_configurations( [], [] );
+		$this->expect_payment_method_configurations_update( [ WC_Stripe_Payment_Methods::CARD, WC_Stripe_Payment_Methods::LINK ], [] );
 
 		$stripe_settings['upe_checkout_experience_enabled'] = 'yes';
 		WC_Stripe_Helper::update_main_stripe_settings( $stripe_settings );
@@ -150,17 +153,19 @@ public function test_turning_on_upe_with_no_stripe_legacy_payment_methods_enable
 		// Because no Stripe LPM's were enabled when UPE was enabled, the Stripe gateway is not enabled yet.
 		$this->assertEquals( 'no', $stripe_settings['enabled'] );
 		$this->assertEquals( 'yes', $stripe_settings['upe_checkout_experience_enabled'] );
-		$this->assertContains( WC_Stripe_Payment_Methods::CARD, $stripe_settings['upe_checkout_experience_accepted_payments'] );
-		$this->assertContains( WC_Stripe_Payment_Methods::LINK, $stripe_settings['upe_checkout_experience_accepted_payments'] );
-		$this->assertCount( 2, $stripe_settings['upe_checkout_experience_accepted_payments'] );
 	}
 
-	public function test_turning_on_upe_enables_the_correct_upe_methods_based_on_which_legacy_payment_methods_were_enabled_and_vice_versa() {
+	public function test_turning_on_upe_enables_the_correct_upe_methods_based_on_which_legacy_payment_methods_were_enabled() {
+		update_option( 'woocommerce_currency', 'EUR' );
 		$this->upe_helper->enable_upe_feature_flag();
 
-		// Enable Alipay and iDEAL LPM gateways.
-		update_option( 'woocommerce_stripe_alipay_settings', [ 'enabled' => 'yes' ] );
+		// Enable the EPS UPE method. Now when UPE is disabled, the EPS LPM should be enabled.
+		$this->mock_payment_method_configurations( [ WC_Stripe_Payment_Methods::EPS, WC_Stripe_Payment_Methods::SEPA_DEBIT, WC_Stripe_Payment_Methods::IDEAL ] );
+
+		// Enable sepa and iDEAL LPM gateways.
+		update_option( 'woocommerce_stripe_sepa_settings', [ 'enabled' => 'yes' ] );
 		update_option( 'woocommerce_stripe_ideal_settings', [ 'enabled' => 'yes' ] );
+		$this->expect_payment_method_configurations_update( [ WC_Stripe_Payment_Methods::SEPA_DEBIT, WC_Stripe_Payment_Methods::IDEAL ], [ WC_Stripe_Payment_Methods::CARD ] );
 		$this->upe_helper->reload_payment_gateways();
 
 		// Initialize default stripe settings, turn on UPE.
@@ -169,20 +174,28 @@ public function test_turning_on_upe_enables_the_correct_upe_methods_based_on_whi
 		$stripe_settings = WC_Stripe_Helper::get_stripe_settings();
 		$this->assertEquals( 'yes', $stripe_settings['enabled'] );
 		$this->assertEquals( 'yes', $stripe_settings['upe_checkout_experience_enabled'] );
-		$this->assertNotContains( WC_Stripe_Payment_Methods::CARD, $stripe_settings['upe_checkout_experience_accepted_payments'] );
-		$this->assertContains( WC_Stripe_Payment_Methods::ALIPAY, $stripe_settings['upe_checkout_experience_accepted_payments'] );
-		$this->assertContains( WC_Stripe_Payment_Methods::IDEAL, $stripe_settings['upe_checkout_experience_accepted_payments'] );
 
-		// Make sure the Alipay and iDEAL LPMs were disabled.
-		$alipay_settings = get_option( 'woocommerce_stripe_alipay_settings' );
-		$this->assertEquals( 'no', $alipay_settings['enabled'] );
+		// Make sure the SEPA and iDEAL LPMs were disabled.
+		$sepa_settings = get_option( 'woocommerce_stripe_sepa_settings' );
+		$this->assertEquals( 'no', $sepa_settings['enabled'] );
 		$ideal_settings = get_option( 'woocommerce_stripe_ideal_settings' );
 		$this->assertEquals( 'no', $ideal_settings['enabled'] );
+	}
 
-		// Enable the EPS UPE method. Now when UPE is disabled, the EPS LPM should be enabled.
-		$stripe_settings['upe_checkout_experience_accepted_payments'][] = WC_Stripe_Payment_Methods::EPS;
+	public function test_turning_off_upe_enables_the_correct_legacy_payment_methods_based_on_which_upe_payment_methods_were_enabled() {
+		update_option( 'woocommerce_currency', 'EUR' );
+		$this->upe_helper->enable_upe_feature_flag();
+
+		// Disable sepa and iDEAL LPM gateways.
+		update_option( 'woocommerce_stripe_sepa_settings', [ 'enabled' => 'no' ] );
+		update_option( 'woocommerce_stripe_ideal_settings', [ 'enabled' => 'no' ] );
+
+		// Turn UPE on first.
+		$stripe_settings['upe_checkout_experience_enabled'] = 'yes';
 		WC_Stripe_Helper::update_main_stripe_settings( $stripe_settings );
 
+		$this->mock_payment_method_configurations( [ WC_Stripe_Payment_Methods::SEPA_DEBIT, WC_Stripe_Payment_Methods::IDEAL ] );
+
 		// Turn UPE off.
 		$stripe_settings['upe_checkout_experience_enabled'] = 'no';
 		WC_Stripe_Helper::update_main_stripe_settings( $stripe_settings );
@@ -191,11 +204,9 @@ public function test_turning_on_upe_enables_the_correct_upe_methods_based_on_whi
 		$stripe_settings = WC_Stripe_Helper::get_stripe_settings();
 		$this->assertEquals( 'no', $stripe_settings['enabled'] );
 		// Check that the correct LPMs were re-enabled.
-		$alipay_settings = get_option( 'woocommerce_stripe_alipay_settings' );
-		$this->assertEquals( 'yes', $alipay_settings['enabled'] );
+		$sepa_settings = get_option( 'woocommerce_stripe_sepa_settings' );
+		$this->assertEquals( 'yes', $sepa_settings['enabled'] );
 		$ideal_settings = get_option( 'woocommerce_stripe_ideal_settings' );
 		$this->assertEquals( 'yes', $ideal_settings['enabled'] );
-		$eps_settings = get_option( 'woocommerce_stripe_eps_settings' );
-		$this->assertEquals( 'yes', $eps_settings['enabled'] );
 	}
 }
diff --git a/tests/phpunit/wc-mock-stripe-api-unit-test-case.php b/tests/phpunit/wc-mock-stripe-api-unit-test-case.php
new file mode 100644
index 0000000000..94fa57ef6c
--- /dev/null
+++ b/tests/phpunit/wc-mock-stripe-api-unit-test-case.php
@@ -0,0 +1,110 @@
+<?php
+/**
+ * This stub assists IDE in recognizing PHPUnit tests.
+ *
+ * @package WooCommerce_Stripe/Tests/WP_UnitTestCase
+ */
+
+/**
+ * WP_UnitTestCase class
+ */
+class WC_Mock_Stripe_API_Unit_Test_Case extends WP_UnitTestCase {
+
+	/**
+	 * @var WC_Stripe_API
+	 */
+	protected $stripe_api;
+
+	/**
+	 * Set up.
+	 */
+	public function set_up() {
+		parent::set_up();
+		$this->stripe_api = $this->createMock( WC_Stripe_API::class );
+		WC_Stripe_API::set_instance( $this->stripe_api );
+	}
+
+	/**
+	 * Tear down.
+	 */
+	public function tear_down() {
+		parent::tear_down();
+		WC_Stripe_Payment_Method_Configurations::reset_primary_configuration();
+	}
+
+	/**
+	 * Expect payment method configuration to be updated with enabled payment method IDs and disabled payment method IDs.
+	 *
+	 * @param array $enabled_payment_method_ids
+	 * @param array $disabled_payment_method_ids
+	 */
+	protected function expect_payment_method_configurations_update( $enabled_payment_method_ids = [], $disabled_payment_method_ids = [] ) {
+		$this->stripe_api->expects( $this->once() )->method( 'update_payment_method_configurations' )->with(
+			$this->equalTo( 'pmc_abcdef' ),
+			$this->callback(
+				function( $actual ) use ( $enabled_payment_method_ids, $disabled_payment_method_ids ) {
+					foreach ( $enabled_payment_method_ids as $payment_method ) {
+						if ( ! isset( $actual[ $payment_method ] ) || 'on' !== $actual[ $payment_method ]['display_preference']['preference'] ) {
+							return false;
+						}
+					}
+					foreach ( $disabled_payment_method_ids as $payment_method ) {
+						if ( ! isset( $actual[ $payment_method ] ) || 'off' !== $actual[ $payment_method ]['display_preference']['preference'] ) {
+							return false;
+						}
+					}
+					return true;
+				}
+			)
+		);
+	}
+
+	/**
+	 * Mock the payment method configurations.
+	 *
+	 * @param array $enabled_payment_method_ids
+	 * @param array $disabled_payment_method_ids
+	 */
+	protected function mock_payment_method_configurations( $enabled_payment_method_ids = [], $disabled_payment_method_ids = [] ) {
+		$payment_method_configuration = [
+			'id'       => 'pmc_abcdef',
+			'object'   => 'payment_method_configuration',
+			'active'   => true,
+			'parent'   => WC_Stripe_Payment_Method_Configurations::TEST_MODE_CONFIGURATION_PARENT_ID,
+			'livemode' => false,
+		];
+
+		foreach ( $enabled_payment_method_ids as $payment_method ) {
+			$payment_method_configuration[ $payment_method ] = (object) [
+				'display_preference' => (object) [ 'value' => 'on' ],
+			];
+		}
+
+		foreach ( $disabled_payment_method_ids as $payment_method ) {
+			$payment_method_configuration[ $payment_method ] = (object) [
+				'display_preference' => (object) [ 'value' => 'off' ],
+			];
+		}
+
+		$this->stripe_api->method( 'get_payment_method_configurations' )->willReturn(
+			(object) [
+				'data' => [
+					(object) $payment_method_configuration,
+				],
+			],
+		);
+	}
+
+	/**
+	 * @param array $account_data
+	 *
+	 * @return void
+	 */
+	protected function set_stripe_account_data( $account_data ) {
+		WC_Stripe::get_instance()->account = $this->getMockBuilder( 'WC_Stripe_Account' )
+												->disableOriginalConstructor()
+												->setMethods( [ 'get_cached_account_data' ] )
+												->getMock();
+		WC_Stripe::get_instance()->account->method( 'get_cached_account_data' )->willReturn( $account_data );
+	}
+}
diff --git a/woocommerce-gateway-stripe.php b/woocommerce-gateway-stripe.php
index 23ae15ca23..fbf3f6de48 100644
--- a/woocommerce-gateway-stripe.php
+++ b/woocommerce-gateway-stripe.php
@@ -198,6 +198,7 @@ public function init() {
 				require_once __DIR__ . '/includes/class-wc-stripe-exception.php';
 				require_once __DIR__ . '/includes/class-wc-stripe-logger.php';
 				require_once __DIR__ . '/includes/class-wc-stripe-helper.php';
+				require_once __DIR__ . '/includes/class-wc-stripe-payment-method-configurations.php';
 				include_once __DIR__ . '/includes/class-wc-stripe-api.php';
 				include_once __DIR__ . '/includes/class-wc-stripe-mode.php';
 				require_once __DIR__ . '/includes/compat/class-wc-stripe-subscriptions-helper.php';
@@ -620,7 +621,7 @@ protected function toggle_upe( $settings, $old_settings ) {
 			}
 
 			protected function enable_upe( $settings ) {
-				$settings['upe_checkout_experience_accepted_payments'] = [];
+				$payment_methods_to_enable = [];
 
 				$payment_gateways = WC_Stripe_Helper::get_legacy_payment_methods();
 				foreach ( WC_Stripe_UPE_Payment_Gateway::UPE_AVAILABLE_METHODS as $method_class ) {
@@ -646,21 +647,24 @@ protected function enable_upe( $settings ) {
 							'yes'
 						);
 						// ENABLE UPE METHOD
-						$settings['upe_checkout_experience_accepted_payments'][] = $method_class::STRIPE_ID;
+						$payment_methods_to_enable[] = $method_class::STRIPE_ID;
 					}
 
 					if ( 'stripe' === $lpm_gateway_id && isset( $this->stripe_gateway ) && $this->stripe_gateway->is_enabled() ) {
-						$settings['upe_checkout_experience_accepted_payments'][] = 'card';
-						$settings['upe_checkout_experience_accepted_payments'][] = 'link';
+						$payment_methods_to_enable[] = 'card';
+						$payment_methods_to_enable[] = 'link';
 					}
 				}
-				if ( empty( $settings['upe_checkout_experience_accepted_payments'] ) ) {
-					$settings['upe_checkout_experience_accepted_payments'] = [ 'card', 'link' ];
+				if ( empty( $payment_methods_to_enable ) ) {
+					$payment_methods_to_enable = [ 'card', 'link' ];
 				} else {
 					// The 'stripe' gateway must be enabled for UPE if any LPMs were enabled.
 					$settings['enabled'] = 'yes';
 				}
 
+				$upe_gateway = new WC_Stripe_UPE_Payment_Gateway();
+				$upe_gateway->update_enabled_payment_methods( $payment_methods_to_enable );
+
 				return $settings;
 			}
 
@@ -689,9 +693,7 @@ protected function disable_upe( $settings ) {
 					$settings['enabled'] = 'no';
 				}
 				// DISABLE ALL UPE METHODS
-				if ( ! isset( $settings['upe_checkout_experience_accepted_payments'] ) ) {
-					$settings['upe_checkout_experience_accepted_payments'] = [];
-				}
+				$upe_gateway->update_enabled_payment_methods( [] );
 				return $settings;
 			}