diff --git a/src/Cli/dotnet/Commands/Run/VirtualProjectBuildingCommand.cs b/src/Cli/dotnet/Commands/Run/VirtualProjectBuildingCommand.cs
index c6ab42bbc498..8558751eafbd 100644
--- a/src/Cli/dotnet/Commands/Run/VirtualProjectBuildingCommand.cs
+++ b/src/Cli/dotnet/Commands/Run/VirtualProjectBuildingCommand.cs
@@ -1180,11 +1180,16 @@ public static void WriteProjectFile(
             // Note that ArtifactsPath needs to be specified before Sdk.props
             // (usually it's recommended to specify it in Directory.Build.props
             // but importing Sdk.props manually afterwards also works).
+            //
+            // An empty value is always given for BaseIntermediateOutputPath and BaseOutputPath, to ensure that
+            // the SDK targets will initialize them based on ArtifactsPath, and not use values for those paths coming in from Directory.Build.props.
             writer.WriteLine($"""
                 <Project>
 
                   <PropertyGroup>
                     <IncludeProjectNameInArtifactsPaths>false</IncludeProjectNameInArtifactsPaths>
+                    <BaseIntermediateOutputPath></BaseIntermediateOutputPath>
+                    <BaseOutputPath></BaseOutputPath>
                     <ArtifactsPath>{EscapeValue(artifactsPath)}</ArtifactsPath>
                     <PublishDir>artifacts/$(MSBuildProjectName)</PublishDir>
                     <PackageOutputPath>artifacts/$(MSBuildProjectName)</PackageOutputPath>
diff --git a/test/dotnet.Tests/CommandTests/Run/RunFileTests.cs b/test/dotnet.Tests/CommandTests/Run/RunFileTests.cs
index 5d7b53c65a3e..82c23728028e 100644
--- a/test/dotnet.Tests/CommandTests/Run/RunFileTests.cs
+++ b/test/dotnet.Tests/CommandTests/Run/RunFileTests.cs
@@ -919,6 +919,39 @@ public void DefaultProps_DirectoryBuildProps()
             .And.HaveStdOutContaining("error CS0103");
     }
 
+    /// <summary>
+    /// 'BaseIntermediateOutputPath'/'BaseOutputPath' specified in Directory.Build.props should effectively be ignored.
+    /// We want the standard logic for determining these from an 'ArtifactsPath' to always be used.
+    /// See also https://github.com/dotnet/sdk/blob/2b9fc02a265c735f2132e4e3626e94962e48bdf5/src/Tasks/Microsoft.NET.Build.Tasks/sdk/UseArtifactsOutputPath.props#L25.
+    /// </summary>
+    [Fact]
+    public void BaseOutputPathProps_FromDirectoryBuildProps_NotUsed()
+    {
+        var testInstance = _testAssetsManager.CreateTestDirectory();
+        File.WriteAllText(Path.Join(testInstance.Path, "Program.cs"), """
+            Console.WriteLine("Hi");
+            """);
+
+        var dbPropsObjPath = Path.Join(testInstance.Path, "MyOutput", "obj");
+        var dbPropsBinPath = Path.Join(testInstance.Path, "MyOutput", "bin");
+        File.WriteAllText(Path.Join(testInstance.Path, "Directory.Build.props"), $"""
+            <Project>
+              <PropertyGroup>
+                <BaseIntermediateOutputPath>{dbPropsObjPath}</BaseIntermediateOutputPath>
+                <BaseOutputPath>{dbPropsBinPath}</BaseOutputPath>
+              </PropertyGroup>
+            </Project>
+            """);
+
+        new DotnetCommand(Log, "run", "Program.cs")
+            .WithWorkingDirectory(testInstance.Path)
+            .Execute()
+            .Should().Pass();
+
+        Assert.False(Directory.Exists(dbPropsObjPath));
+        Assert.False(Directory.Exists(dbPropsBinPath));
+    }
+
     /// <summary>
     /// Overriding default (implicit) properties of file-based apps from custom SDKs.
     /// </summary>