diff --git a/actions/setup/js/push_to_pull_request_branch.cjs b/actions/setup/js/push_to_pull_request_branch.cjs
index 5454a7e4bb..6aecf628af 100644
--- a/actions/setup/js/push_to_pull_request_branch.cjs
+++ b/actions/setup/js/push_to_pull_request_branch.cjs
@@ -603,9 +603,17 @@ async function main(config = {}) {
           await exec.exec("git", ["fetch", bundleFilePath, `refs/heads/${message.branch}:${bundleRef}`], baseGitOpts);
           core.info(`Fetched bundle to ${bundleRef}`);
 
-          // Fast-forward the current branch to the bundle tip
-          await exec.exec("git", ["merge", "--ff-only", bundleRef], baseGitOpts);
-          core.info("Fast-forwarded branch to bundle tip");
+          // Point the checked-out branch at the bundle tip directly. In shallow
+          // checkouts, merge --ff-only can fail to discover the ancestry even
+          // when the bundle tip is based on the current branch tip and the
+          // prerequisite exists locally.
+          const updateRefArgs = ["update-ref", `refs/heads/${branchName}`, bundleRef];
+          if (remoteHeadBeforePatch) {
+            updateRefArgs.push(remoteHeadBeforePatch);
+          }
+          await exec.exec("git", updateRefArgs, baseGitOpts);
+          await exec.exec("git", ["reset", "--hard"], baseGitOpts);
+          core.info("Updated branch to bundle tip");
 
           // Clean up the temporary ref
           try {
diff --git a/actions/setup/js/push_to_pull_request_branch.test.cjs b/actions/setup/js/push_to_pull_request_branch.test.cjs
index 486573ddd1..075a6f7edc 100644
--- a/actions/setup/js/push_to_pull_request_branch.test.cjs
+++ b/actions/setup/js/push_to_pull_request_branch.test.cjs
@@ -1199,6 +1199,40 @@ index 0000000..abc1234
     });
   });
 
+  // ──────────────────────────────────────────────────────
+  // Bundle Transport Application
+  // ──────────────────────────────────────────────────────
+
+  describe("bundle transport application", () => {
+    it("should apply bundle transport by updating the branch ref instead of merging", async () => {
+      const bundlePath = path.join(tempDir, "test.bundle");
+      const patchPath = createPatchFile("small patch content");
+      fs.writeFileSync(bundlePath, "bundle content");
+
+      const pushSignedCommitsModule = require("./push_signed_commits.cjs");
+      const pushSignedSpy = vi.spyOn(pushSignedCommitsModule, "pushSignedCommits").mockResolvedValue("bundle-tip");
+
+      try {
+        mockExec.getExecOutput
+          .mockResolvedValueOnce({ exitCode: 0, stdout: "remote-head\trefs/heads/feature-branch\n", stderr: "" }) // preflight ls-remote
+          .mockResolvedValueOnce({ exitCode: 0, stdout: "remote-head\n", stderr: "" }) // rev-parse HEAD before bundle
+          .mockResolvedValueOnce({ exitCode: 0, stdout: "2\n", stderr: "" }); // rev-list --count
+
+        const module = await loadModule();
+        const handler = await module.main({});
+        const result = await handler({ branch: "feature-branch", patch_path: patchPath, bundle_path: bundlePath, diff_size: 5 * 1024 }, {});
+
+        expect(result.success).toBe(true);
+        expect(mockExec.exec).toHaveBeenCalledWith("git", ["fetch", bundlePath, "refs/heads/feature-branch:refs/bundles/push-feature-branch"], expect.any(Object));
+        expect(mockExec.exec).toHaveBeenCalledWith("git", ["update-ref", "refs/heads/feature-branch", "refs/bundles/push-feature-branch", "remote-head"], expect.any(Object));
+        expect(mockExec.exec).toHaveBeenCalledWith("git", ["reset", "--hard"], expect.any(Object));
+        expect(mockExec.exec).not.toHaveBeenCalledWith("git", ["merge", "--ff-only", "refs/bundles/push-feature-branch"], expect.any(Object));
+      } finally {
+        pushSignedSpy.mockRestore();
+      }
+    });
+  });
+
   // ──────────────────────────────────────────────────────
   // Title Prefix and Labels Validation
   // ──────────────────────────────────────────────────────