diff --git a/packages/coverage-istanbul/src/provider.ts b/packages/coverage-istanbul/src/provider.ts
index 2934ee82e486..f07eab33ae1d 100644
--- a/packages/coverage-istanbul/src/provider.ts
+++ b/packages/coverage-istanbul/src/provider.ts
@@ -199,9 +199,9 @@ export class IstanbulCoverageProvider extends BaseCoverageProvider<ResolvedCover
   }
 
   async parseConfigModule(configFilePath: string): Promise<ProxifiedModule<any>> {
-    return parseModule(
-      await fs.readFile(configFilePath, 'utf8'),
-    )
+    const contents = await fs.readFile(configFilePath, 'utf8')
+
+    return parseModule(`${contents}${this.autoUpdateMarker}`)
   }
 
   private async getCoverageMapForUncoveredFiles(coveredFiles: string[]) {
diff --git a/packages/coverage-v8/src/provider.ts b/packages/coverage-v8/src/provider.ts
index 2d68e337ccd1..c883bdae74ab 100644
--- a/packages/coverage-v8/src/provider.ts
+++ b/packages/coverage-v8/src/provider.ts
@@ -139,9 +139,9 @@ export class V8CoverageProvider extends BaseCoverageProvider<ResolvedCoverageOpt
   }
 
   async parseConfigModule(configFilePath: string): Promise<ProxifiedModule<any>> {
-    return parseModule(
-      await fs.readFile(configFilePath, 'utf8'),
-    )
+    const contents = await fs.readFile(configFilePath, 'utf8')
+
+    return parseModule(`${contents}${this.autoUpdateMarker}`)
   }
 
   private async getCoverageMapForUncoveredFiles(testedFiles: string[]): Promise<CoverageMap> {
diff --git a/packages/vitest/src/node/coverage.ts b/packages/vitest/src/node/coverage.ts
index e81fd0e4875e..49fe4cc483dc 100644
--- a/packages/vitest/src/node/coverage.ts
+++ b/packages/vitest/src/node/coverage.ts
@@ -77,6 +77,7 @@ export class BaseCoverageProvider<Options extends ResolvedCoverageOptions<'istan
   version!: string
   options!: Options
   globCache: Map<string, boolean> = new Map()
+  autoUpdateMarker = '\n// __VITEST_COVERAGE_MARKER__'
 
   coverageFiles: CoverageFiles = new Map()
   pendingPromises: Promise<void>[] = []
@@ -360,7 +361,7 @@ export class BaseCoverageProvider<Options extends ResolvedCoverageOptions<'istan
         onUpdate: () =>
           writeFileSync(
             configFilePath,
-            configModule.generate().code,
+            configModule.generate().code.replace(this.autoUpdateMarker, ''),
             'utf-8',
           ),
 
diff --git a/test/coverage-test/test/threshold-auto-update.test.ts b/test/coverage-test/test/threshold-auto-update.test.ts
index b73ddfcef8fc..e3553f5705f4 100644
--- a/test/coverage-test/test/threshold-auto-update.test.ts
+++ b/test/coverage-test/test/threshold-auto-update.test.ts
@@ -65,7 +65,8 @@ test('thresholds.autoUpdate updates thresholds', async () => {
           }
         }
       },
-    })"
+    })
+    "
   `)
 })