diff --git a/src/mount.ts b/src/mount.ts
index ec5e08332..141fb8571 100644
--- a/src/mount.ts
+++ b/src/mount.ts
@@ -45,7 +45,7 @@ import { attachEmitListener } from './emit'
 import { createVNodeTransformer } from './vnodeTransformers/util'
 import {
   createStubComponentsTransformer,
-  addToDoNotStubComponents
+  CreateStubComponentsTransformerConfig
 } from './vnodeTransformers/stubComponentsTransformer'
 import { createStubDirectivesTransformer } from './vnodeTransformers/stubDirectivesTransformer'
 import {
@@ -315,6 +315,9 @@ export function mount(
   let component: ConcreteComponent
   const instanceOptions = getInstanceOptions(options ?? {})
 
+  const rootComponents: CreateStubComponentsTransformerConfig['rootComponents'] =
+    {}
+
   if (
     isFunctionalComponent(originalComponent) ||
     isLegacyFunctionalComponent(originalComponent)
@@ -335,15 +338,14 @@ export function mount(
           h(originalComponent, { ...props, ...attrs }, slots),
       ...instanceOptions
     })
-    addToDoNotStubComponents(originalComponent)
+    rootComponents.legacy = originalComponent
   } else if (isObjectComponent(originalComponent)) {
     component = { ...originalComponent, ...instanceOptions }
   } else {
     component = originalComponent
   }
 
-  // Don't stub component only on root level, but still stub if used inside
-  addToDoNotStubComponents(component, true)
+  rootComponents.component = component
   // We've just replaced our component with its copy
   // Let's register it as a stub so user can find it
   registerStub({ source: originalComponent, stub: component })
@@ -465,11 +467,6 @@ export function mount(
 
   // create the app
   const app = createApp(Parent)
-  // the Parent type must not be stubbed
-  // but we can't add it directly, as createApp creates a copy
-  // and store it in app._component (since v3.2.32)
-  // So we store this one instead
-  addToDoNotStubComponents(app._component)
 
   // add tracking for emitted events
   // this must be done after `createApp`: https://github.com/vuejs/test-utils/issues/436
@@ -577,6 +574,7 @@ export function mount(
     createVNodeTransformer({
       transformers: [
         createStubComponentsTransformer({
+          rootComponents,
           stubs: getComponentsFromStubs(global.stubs),
           shallow: options?.shallow,
           renderStubDefaultSlot: global.renderStubDefaultSlot
diff --git a/src/vnodeTransformers/stubComponentsTransformer.ts b/src/vnodeTransformers/stubComponentsTransformer.ts
index 75da6b513..6ade69577 100644
--- a/src/vnodeTransformers/stubComponentsTransformer.ts
+++ b/src/vnodeTransformers/stubComponentsTransformer.ts
@@ -36,15 +36,6 @@ interface StubOptions {
   renderStubDefaultSlot?: boolean
 }
 
-const doNotStubComponents = new WeakMap<ConcreteComponent, boolean>()
-const shouldNotStub = (type: ConcreteComponent) => doNotStubComponents.has(type)
-const shouldNotStubRoot = (type: ConcreteComponent) =>
-  !!doNotStubComponents.get(type)
-export const addToDoNotStubComponents = (
-  type: ConcreteComponent,
-  onlyRoot?: boolean
-) => doNotStubComponents.set(type, !!onlyRoot)
-
 const normalizeStubProps = (props: ComponentPropsOptions) => {
   // props are always normalized to object syntax
   const $props = props as unknown as ComponentObjectPropsOptions
@@ -106,13 +97,18 @@ const resolveComponentStubByName = (
   }
 }
 
-interface CreateStubComponentsTransformerConfig {
+export interface CreateStubComponentsTransformerConfig {
+  rootComponents: {
+    legacy?: Component
+    component?: Component
+  }
   stubs?: Record<string, Component | boolean>
   shallow?: boolean
   renderStubDefaultSlot: boolean
 }
 
 export function createStubComponentsTransformer({
+  rootComponents,
   stubs = {},
   shallow = false,
   renderStubDefaultSlot = false
@@ -166,11 +162,15 @@ export function createStubComponentsTransformer({
       })
     }
 
-    if (shouldNotStub(type)) {
-      // Either don't stub everytime or only on root level
-      if (!instance?.parent || !shouldNotStubRoot(type)) {
-        return type
-      }
+    if (
+      // Don't stub VTU_ROOT component
+      !instance ||
+      // Don't stub mounted component on root level
+      (rootComponents.component === type && !instance?.parent) ||
+      // Don't stub component with compat wrapper
+      (rootComponents.legacy && rootComponents.legacy === type)
+    ) {
+      return type
     }
 
     const registeredName = getComponentRegisteredName(instance, type)
@@ -225,7 +225,7 @@ export function createStubComponentsTransformer({
       // Set name when using shallow without stub
       const stubName = name || registeredName || componentName
 
-      const newStub =
+      return (
         config.plugins.createStubs?.({
           name: stubName,
           component: type
@@ -235,7 +235,7 @@ export function createStubComponentsTransformer({
           type,
           renderStubDefaultSlot
         })
-      return newStub
+      )
     }
 
     return type