diff --git a/packages/vitest/src/runtime/moduleRunner/moduleRunner.ts b/packages/vitest/src/runtime/moduleRunner/moduleRunner.ts
index be655b57f8af..c81b5ee89aee 100644
--- a/packages/vitest/src/runtime/moduleRunner/moduleRunner.ts
+++ b/packages/vitest/src/runtime/moduleRunner/moduleRunner.ts
@@ -168,23 +168,29 @@ export class VitestModuleRunner
     if (mod.meta && 'mockedModule' in mod.meta) {
       const mockedModule = mod.meta.mockedModule as MockedModule
       const mockId = this.mocker.getMockPath(mod.id)
+      const currentMock = this.mocker.getDependencyMock(mod.id)
       // bypass mock and force "importActual" behavior when:
       // - mock was removed by doUnmock (stale mockedModule in meta)
+      if (!currentMock) {
+        const node = await this.fetchModule(injectQuery(url, '_vitest_original'))
+        return this._cachedRequest(node.url, node, callstack, metadata)
+      }
       // - self-import: mock factory/file is importing the module it's mocking
-      const isStale = !this.mocker.getDependencyMock(mod.id)
       const isSelfImport = callstack.includes(mockId)
         || callstack.includes(url)
-        || ('redirect' in mockedModule && callstack.includes(mockedModule.redirect))
-      if (isStale || isSelfImport) {
+        || ('redirect' in currentMock && callstack.includes(currentMock.redirect))
+      if (isSelfImport) {
         const node = await this.fetchModule(injectQuery(url, '_vitest_original'))
         return this._cachedRequest(node.url, node, callstack, metadata)
       }
-      mocked = await this.mocker.requestWithMockedModule(
-        url,
-        mod,
-        callstack,
-        mockedModule,
-      )
+      const isAutoMock = currentMock.type === 'automock' || currentMock.type === 'autospy'
+      if (isAutoMock && currentMock !== mockedModule) {
+        const freshNode = await this.fetchModule(injectQuery(url, '_vitest_original'))
+        mocked = await this.mocker.requestWithMockedModule(url, freshNode, callstack, currentMock)
+      }
+      else {
+        mocked = await this.mocker.requestWithMockedModule(url, mod, callstack, currentMock)
+      }
     }
     else {
       mocked = await this.mocker.mockedRequest(url, mod, callstack)
diff --git a/test/e2e/test/mocking.test.ts b/test/e2e/test/mocking.test.ts
index fe2e55bc7d4a..f99717878a73 100644
--- a/test/e2e/test/mocking.test.ts
+++ b/test/e2e/test/mocking.test.ts
@@ -3,7 +3,7 @@ import path from 'node:path'
 import { playwright } from '@vitest/browser-playwright'
 import { expect, test } from 'vitest'
 import { rolldownVersion } from 'vitest/node'
-import { runInlineTests, runVitest } from '../../test-utils'
+import { runInlineTests, runVitest, StableTestFileOrderSorter } from '../../test-utils'
 
 test('setting resetMocks works if restoreMocks is also set', async () => {
   const { stderr, testTree } = await runInlineTests({
@@ -510,3 +510,65 @@ test("local", async () => {
     }
   `)
 })
+
+test('automocking works with isolate:false when factory mock runs first (resolve alias)', async () => {
+  const { stderr, testTree } = await runInlineTests({
+    'vitest.config.js': `
+import path from 'node:path'
+import { defineConfig } from 'vitest/config'
+
+export default defineConfig({
+  resolve: {
+    alias: {
+      '~': path.resolve(import.meta.dirname, 'src'),
+    },
+  },
+  test: {
+    isolate: false,
+  },
+})
+    `,
+    './src/dep.ts': `
+export function useDep(): string { return 'real' }
+export function helperDep(): number { return 42 }
+    `,
+    './a-factory.test.ts': `
+import { vi, test, expect } from 'vitest'
+import { useDep } from '~/dep'
+vi.mock(import('~/dep'), () => ({
+  useDep: () => 'factory',
+  helperDep: () => 0,
+}))
+test('factory mock', () => {
+  expect(useDep()).toBe('factory')
+})
+    `,
+    './b-automock.test.ts': `
+import { vi, test, expect } from 'vitest'
+import { useDep } from '~/dep'
+vi.mock(import('~/dep'))
+test('automock exports are mock functions', () => {
+  expect(vi.isMockFunction(useDep)).toBe(true)
+})
+test('automock mockReturnValue works', () => {
+  vi.mocked(useDep).mockReturnValue('mocked')
+  expect(useDep()).toBe('mocked')
+})
+    `,
+  }, {
+    sequence: { sequencer: StableTestFileOrderSorter },
+  })
+
+  expect(stderr).toBe('')
+  expect(testTree()).toMatchInlineSnapshot(`
+    {
+      "a-factory.test.ts": {
+        "factory mock": "passed",
+      },
+      "b-automock.test.ts": {
+        "automock exports are mock functions": "passed",
+        "automock mockReturnValue works": "passed",
+      },
+    }
+  `)
+})