diff --git a/src/Mvc/test/Mvc.FunctionalTests/TestingInfrastructureInheritanceTests.cs b/src/Mvc/test/Mvc.FunctionalTests/TestingInfrastructureInheritanceTests.cs
index b50e3be4a43c..fb9b226c35a1 100644
--- a/src/Mvc/test/Mvc.FunctionalTests/TestingInfrastructureInheritanceTests.cs
+++ b/src/Mvc/test/Mvc.FunctionalTests/TestingInfrastructureInheritanceTests.cs
@@ -25,12 +25,13 @@ public void TestingInfrastructure_WebHost_WithWebHostBuilderRespectsCustomizatio
 
         // Assert
         Assert.Equal(new[] { "ConfigureWebHost", "Customization", "FurtherCustomization" }, factory.ConfigureWebHostCalled.ToArray());
-        Assert.True(factory.CreateServerCalled);
-        Assert.False(factory.CreateWebHostBuilderCalled);
+        Assert.True(factory.CreateServerIWebHostBuilderCalled);
+        Assert.False(factory.CreateServerWithServiceProviderCalled);
+        Assert.True(factory.CreateWebHostBuilderCalled);
         // GetTestAssemblies is not called when reading content roots from MvcAppManifest
         Assert.False(factory.GetTestAssembliesCalled);
         Assert.True(factory.CreateHostBuilderCalled);
-        Assert.True(factory.CreateHostCalled);
+        Assert.False(factory.CreateHostCalled);
     }
 
     [Fact]
@@ -48,7 +49,8 @@ public void TestingInfrastructure_GenericHost_WithWithHostBuilderRespectsCustomi
         Assert.False(factory.GetTestAssembliesCalled);
         Assert.True(factory.CreateHostBuilderCalled);
         Assert.True(factory.CreateHostCalled);
-        Assert.True(factory.CreateServerCalled);
+        Assert.False(factory.CreateServerIWebHostBuilderCalled);
+        Assert.True(factory.CreateServerWithServiceProviderCalled);
         Assert.False(factory.CreateWebHostBuilderCalled);
     }
 
@@ -108,6 +110,23 @@ public void TestingInfrastructure_GenericHost_HostDispose()
         Assert.True(sink._asyncDisposed);
     }
 
+    [Fact]
+    public void TestingInfrastructure_WebApplicationBuilder_RespectsCustomizations()
+    {
+        // Arrange
+        using var factory = new CustomizedFactory<SimpleWebSiteWithWebApplicationBuilder.Program>();
+        factory.StartServer();
+
+        // Assert
+        Assert.Equal(["ConfigureWebHost"], factory.ConfigureWebHostCalled.ToArray());
+        Assert.False(factory.GetTestAssembliesCalled);
+        Assert.True(factory.CreateHostBuilderCalled);
+        Assert.True(factory.CreateHostCalled);
+        Assert.False(factory.CreateServerIWebHostBuilderCalled);
+        Assert.True(factory.CreateServerWithServiceProviderCalled);
+        Assert.True(factory.CreateWebHostBuilderCalled);
+    }
+
     private static void ConfigureWebHostBuilder(IWebHostBuilder builder) =>
         builder.UseStartup<GenericHostWebSite.Startup>()
         .ConfigureServices(s => s.AddScoped<DisposableService>());
@@ -131,7 +150,8 @@ private class CustomizedFactory<TEntryPoint> : WebApplicationFactory<TEntryPoint
         public bool GetTestAssembliesCalled { get; private set; }
         public bool CreateWebHostBuilderCalled { get; private set; }
         public bool CreateHostBuilderCalled { get; private set; }
-        public bool CreateServerCalled { get; private set; }
+        public bool CreateServerIWebHostBuilderCalled { get; private set; }
+        public bool CreateServerWithServiceProviderCalled { get; private set; }
         public bool CreateHostCalled { get; private set; }
         public IList<string> ConfigureWebHostCalled { get; private set; } = new List<string>();
 
@@ -143,13 +163,13 @@ protected override void ConfigureWebHost(IWebHostBuilder builder)
 
         protected override TestServer CreateServer(IWebHostBuilder builder)
         {
-            CreateServerCalled = true;
+            CreateServerIWebHostBuilderCalled = true;
             return base.CreateServer(builder);
         }
 
         protected override TestServer CreateServer(IServiceProvider serviceProvider)
         {
-            CreateServerCalled = true;
+            CreateServerWithServiceProviderCalled = true;
             return base.CreateServer(serviceProvider);
         }
 
diff --git a/src/Mvc/test/WebSites/BasicWebSite/Program.cs b/src/Mvc/test/WebSites/BasicWebSite/Program.cs
index a73dd5d7b4b4..c0e77a1028e0 100644
--- a/src/Mvc/test/WebSites/BasicWebSite/Program.cs
+++ b/src/Mvc/test/WebSites/BasicWebSite/Program.cs
@@ -9,21 +9,19 @@ public class Program
 {
     public static void Main(string[] args)
     {
-        using var host = CreateHostBuilder(args).Build();
+        using var host = CreateWebHostBuilder(args).Build();
         host.Run();
     }
 
-    // This method now returns IHostBuilder and uses the new pattern with HostBuilder and ConfigureWebHost
-    public static IHostBuilder CreateHostBuilder(string[] args) =>
-        new HostBuilder()
-            .ConfigureWebHost(webHostBuilder =>
-            {
-                webHostBuilder
-                    .UseContentRoot(Directory.GetCurrentDirectory())
-                    .UseStartup<StartupWithoutEndpointRouting>()
-                    .UseKestrel()
-                    .UseIISIntegration();
-            });
+    // Using WebHostBuilder to keep some test coverage in WebApplicationFactory tests
+    public static IWebHostBuilder CreateWebHostBuilder(string[] args) =>
+#pragma warning disable ASPDEPR004 // Type or member is obsolete
+        new WebHostBuilder()
+#pragma warning restore ASPDEPR004 // Type or member is obsolete
+            .UseContentRoot(Directory.GetCurrentDirectory())
+            .UseStartup<StartupWithoutEndpointRouting>()
+            .UseKestrel()
+            .UseIISIntegration();
 }
 
 public class TestService