diff --git a/.changeset/strong-readers-think.md b/.changeset/strong-readers-think.md
new file mode 100644
index 0000000000..1a9aa70b24
--- /dev/null
+++ b/.changeset/strong-readers-think.md
@@ -0,0 +1,6 @@
+---
+"@pnpm/config": patch
+"pnpm": patch
+---
+
+Fix a bug in which specifying `filter` on `pnpm-workspace.yaml` would cause pnpm to not detect any projects.
diff --git a/config/config/src/index.ts b/config/config/src/index.ts
index 12649a22ee..2a04b793c6 100644
--- a/config/config/src/index.ts
+++ b/config/config/src/index.ts
@@ -367,7 +367,7 @@ export async function getConfig (opts: {
     if (pnpmConfig.workspaceDir != null) {
       const workspaceManifest = await readWorkspaceManifest(pnpmConfig.workspaceDir)
 
-      pnpmConfig.workspacePackagePatterns = cliOptions['workspace-packages'] as string[] ?? workspaceManifest?.packages ?? ['.']
+      pnpmConfig.workspacePackagePatterns = cliOptions['workspace-packages'] as string[] ?? workspaceManifest?.packages
       if (workspaceManifest) {
         const newSettings = Object.assign(getOptionsFromPnpmSettings(pnpmConfig.workspaceDir, workspaceManifest, pnpmConfig.rootProjectManifest), configFromCliOpts)
         for (const [key, value] of Object.entries(newSettings)) {
diff --git a/pnpm/test/recursive/misc.ts b/pnpm/test/recursive/misc.ts
index 89dff9b3fe..52e1e42e23 100644
--- a/pnpm/test/recursive/misc.ts
+++ b/pnpm/test/recursive/misc.ts
@@ -314,7 +314,9 @@ test('recursive command with filter from config', async () => {
   ])
 
   fs.writeFileSync('package.json', '{}', 'utf8')
-  fs.writeFileSync('.npmrc', 'filter=project-1 project-2', 'utf8')
+  writeYamlFile('pnpm-workspace.yaml', {
+    filter: ['project-1', 'project-2'],
+  })
   await execPnpm(['recursive', 'install'])
 
   projects['project-1'].has('is-positive')