diff --git a/packages/vitest/src/node/cache/fsModuleCache.ts b/packages/vitest/src/node/cache/fsModuleCache.ts
index b1820f4b4..3063a4dda 100644
--- a/packages/vitest/src/node/cache/fsModuleCache.ts
+++ b/packages/vitest/src/node/cache/fsModuleCache.ts
@@ -146,7 +146,6 @@ export class FileSystemModuleCache {
 
     return {
       id: meta.id,
-      url: meta.url,
       file: meta.file,
       code,
       imports: meta.imports,
@@ -169,7 +168,6 @@ export class FileSystemModuleCache {
       const result = {
         file: fetchResult.file,
         id: fetchResult.id,
-        url: fetchResult.url,
         imports,
         mappings,
         moduleType: fetchResult.moduleType,
@@ -411,7 +409,6 @@ export async function atomicWriteFile(realFilePath: string, data: string): Promi
 }
 
 export interface CachedInlineModuleMeta {
-  url: string
   id: string
   file: string | null
   code: string
diff --git a/packages/vitest/src/node/environments/transformService.ts b/packages/vitest/src/node/environments/transformService.ts
index e82ad41b5..3a9cedbc4 100644
--- a/packages/vitest/src/node/environments/transformService.ts
+++ b/packages/vitest/src/node/environments/transformService.ts
@@ -83,8 +83,10 @@ export class ModuleTransformService {
    */
   async transform(id: string, environment: DevEnvironment): Promise<TransformResult | null> {
     await this.traces.waitInit()
+    // the module graph keeps the url of the first request, so it has to be the url that workers import
+    const url = normalizeResolvedIdToUrl(environment, id)
     const result = await this.traces.$('vitest.module.transform', (span) =>
-      this.fetchInSpan(span, id, undefined, environment),
+      this.fetchInSpan(span, url, undefined, environment),
     )
     // externalized modules are loaded by Node without a transform, like in a normal run
     if ('externalize' in result) {
@@ -96,7 +98,7 @@ export class ModuleTransformService {
         return transformResult
       }
     }
-    return environment.transformRequest(id)
+    return environment.transformRequest(url)
   }
 
   private async fetchInSpan(
@@ -400,7 +402,7 @@ export class ModuleTransformService {
       file: cachedModule.file,
       id: cachedModule.id,
       tmp: cachePath,
-      url: cachedModule.url,
+      url: moduleGraphModule.url,
       invalidate: false,
       moduleType,
     }
diff --git a/test/e2e/test/caching.test.ts b/test/e2e/test/caching.test.ts
index a59b57633..4c0007cb3 100644
--- a/test/e2e/test/caching.test.ts
+++ b/test/e2e/test/caching.test.ts
@@ -267,6 +267,52 @@ test('filtering by related sources reuses the cache', async () => {
   delete (globalThis as any).__vitest_transformed__
 })
 
+test('filtering by related sources runs setup files before every non-isolated file', async () => {
+  const testFile = `
+    import { expect, test } from 'vitest'
+    import './dep.js'
+
+    const setupRuns = globalThis.setupRuns
+    globalThis.testFiles = (globalThis.testFiles ?? 0) + 1
+
+    test('setup file ran before this file', () => {
+      expect(setupRuns).toBe(globalThis.testFiles)
+    })
+  `
+  const related = await runInlineTests(
+    {
+      'vitest.config.js': {
+        test: {
+          isolate: false,
+          setupFiles: ['./setup.js'],
+          fsModuleCache: true,
+          fsModuleCachePath: './node_modules/.vitest-fs-cache',
+        },
+      },
+      'setup.js': `globalThis.setupRuns = (globalThis.setupRuns ?? 0) + 1`,
+      'dep.js': `export const value = 1`,
+      'a.test.js': testFile,
+      'b.test.js': testFile,
+    },
+    { related: ['dep.js'] },
+  )
+  const cached = await runVitest({ root: related.root })
+
+  for (const run of [related, cached]) {
+    expect(run.stderr).toBe('')
+    expect(run.errorTree()).toMatchInlineSnapshot(`
+      {
+        "a.test.js": {
+          "setup file ran before this file": "passed",
+        },
+        "b.test.js": {
+          "setup file ran before this file": "passed",
+        },
+      }
+    `)
+  }
+})
+
 test('if cache key generator bails out, the file is not cached', async () => {
   process.env.REPLACED = 'value1'