diff --git a/packages/extension/src/api.ts b/packages/extension/src/api.ts
index 1bfa30e8..635a8a04 100644
--- a/packages/extension/src/api.ts
+++ b/packages/extension/src/api.ts
@@ -120,6 +120,7 @@ export class VitestFolderAPI {
   readonly workspaceFolder: vscode.WorkspaceFolder
 
   private handlers: ResolvedMeta['handlers']
+  private packageCwds: string[] = []
 
   public createDate = Date.now()
 
@@ -134,6 +135,10 @@ export class VitestFolderAPI {
     this.tag = new vscode.TestTag(pkg.prefix)
   }
 
+  setPackageCwds(cwds: string[]) {
+    this.packageCwds = cwds
+  }
+
   get processId() {
     return this.process.id
   }
@@ -183,7 +188,22 @@ export class VitestFolderAPI {
   }
 
   getFiles() {
-    return this.meta.rpc.getFiles()
+    const files = this.meta.rpc.getFiles()
+    const isWorkspace = !!this.package.workspaceFile && !this.package.configFile
+
+    if (isWorkspace && this.packageCwds.length > 0) {
+      // Filter out files that belong to packages with their own configs
+      return files.then((fileList) => {
+        return fileList.filter(([file]) => {
+          const normalizedFile = normalize(file)
+          // Keep file if it's not in any package directory
+          const isInPackageDir = this.packageCwds.some(cwd => normalizedFile.startsWith(cwd))
+          return !isInPackageDir
+        })
+      })
+    }
+
+    return files
   }
 
   onFileCreated = createQueuedHandler(async (files: string[]) => {
@@ -381,6 +401,17 @@ export async function resolveVitestAPI(workspaceConfigs: VitestPackage[], config
     showVitestError('The extension could not load some configs')
   }
 
+  // Collect package cwds and set them on workspace APIs for filtering
+  const packageCwds = apis
+    .filter(api => !!api.package.configFile && !api.package.workspaceFile)
+    .map(api => normalize(api.package.cwd))
+
+  if (packageCwds.length > 0) {
+    apis
+      .filter(api => !!api.package.workspaceFile && !api.package.configFile)
+      .forEach(api => api.setPackageCwds(packageCwds))
+  }
+
   return new VitestAPI(apis)
 }