diff --git a/.changeset/upset-badgers-dance.md b/.changeset/upset-badgers-dance.md
new file mode 100644
index 0000000000..5d58fcfd97
--- /dev/null
+++ b/.changeset/upset-badgers-dance.md
@@ -0,0 +1,8 @@
+---
+"@pnpm/config": patch
+"pnpm": patch
+---
+
+Reverted a fix shipped in v10.29.1, which caused another issue [#10571](https://github.com/pnpm/pnpm/issues/10571).
+Reverted fix: Fixed pnpm run -r failing with "No projects matched the filters" when an empty pnpm-workspace.yaml exists [#10497](https://github.com/pnpm/pnpm/issues/10497).
+
diff --git a/config/config/src/index.ts b/config/config/src/index.ts
index 2a04b793c6..12649a22ee 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/src/main.ts b/pnpm/src/main.ts
index 527441d9e8..6a478b1adf 100644
--- a/pnpm/src/main.ts
+++ b/pnpm/src/main.ts
@@ -213,7 +213,7 @@ export async function main (inputArgv: string[]): Promise<void> {
     const relativeWSDirPath = () => path.relative(process.cwd(), wsDir) || '.'
     if (config.workspaceRoot) {
       filters.push({ filter: `{${relativeWSDirPath()}}`, followProdDepsOnly: Boolean(config.filterProd.length) })
-    } else if (filters.length === 0 && workspaceDir && config.workspacePackagePatterns && !config.includeWorkspaceRoot && (cmd === 'run' || cmd === 'exec' || cmd === 'add' || cmd === 'test')) {
+    } else if (filters.length === 0 && workspaceDir && !config.includeWorkspaceRoot && (cmd === 'run' || cmd === 'exec' || cmd === 'add' || cmd === 'test')) {
       filters.push({ filter: `!{${relativeWSDirPath()}}`, followProdDepsOnly: Boolean(config.filterProd.length) })
     }
 
diff --git a/pnpm/test/monorepo/index.ts b/pnpm/test/monorepo/index.ts
index 4301a2ba45..07339ca830 100644
--- a/pnpm/test/monorepo/index.ts
+++ b/pnpm/test/monorepo/index.ts
@@ -61,22 +61,6 @@ test('no projects found', async () => {
   }
 })
 
-test('empty pnpm-workspace.yaml should not break pnpm run -r', async () => {
-  prepare({
-    name: 'project',
-    version: '1.0.0',
-    scripts: {
-      test: 'echo Passed',
-    },
-  })
-
-  fs.writeFileSync('pnpm-workspace.yaml', '')
-
-  const { stdout, status } = execPnpmSync(['run', '-r', 'test'])
-  expect(status).toBe(0)
-  expect(stdout.toString()).toContain('Passed')
-})
-
 const invalidWorkspaceManifests = [
   'pnpm-workspaces.yaml',
   'pnpm-workspaces.yml',