diff --git a/packages/cli/snap-tests-global/migration-monorepo-yarn4/snap.txt b/packages/cli/snap-tests-global/migration-monorepo-yarn4/snap.txt
index d29b5d8f55..aa5c45c326 100644
--- a/packages/cli/snap-tests-global/migration-monorepo-yarn4/snap.txt
+++ b/packages/cli/snap-tests-global/migration-monorepo-yarn4/snap.txt
@@ -71,7 +71,7 @@ export default defineConfig({
 }
 
 > cat .yarnrc.yml # check .yarnrc.yml
-nodeLinker: node-modules
+nodeLinker: pnpm
 catalog:
   vite: npm:@voidzero-dev/vite-plus-core@latest
   vitest: npm:@voidzero-dev/vite-plus-test@latest
diff --git a/packages/cli/src/create/__tests__/utils.spec.ts b/packages/cli/src/create/__tests__/utils.spec.ts
index ecec51f39c..8a0d379c75 100644
--- a/packages/cli/src/create/__tests__/utils.spec.ts
+++ b/packages/cli/src/create/__tests__/utils.spec.ts
@@ -352,12 +352,12 @@ describe('renameFiles', () => {
 
   it('renames `_npmrc` and `_yarnrc.yml`', () => {
     write('_npmrc', 'auto-install-peers=true\n');
-    write('_yarnrc.yml', 'nodeLinker: node-modules\n');
+    write('_yarnrc.yml', 'nodeLinker: pnpm\n');
     renameFiles(projectDir);
     expect(exists('_npmrc')).toBe(false);
     expect(exists('_yarnrc.yml')).toBe(false);
     expect(read('.npmrc')).toBe('auto-install-peers=true\n');
-    expect(read('.yarnrc.yml')).toBe('nodeLinker: node-modules\n');
+    expect(read('.yarnrc.yml')).toBe('nodeLinker: pnpm\n');
   });
 
   it('is a no-op when no source files exist', () => {
diff --git a/packages/cli/src/create/bin.ts b/packages/cli/src/create/bin.ts
index feb23261d8..daf407768d 100644
--- a/packages/cli/src/create/bin.ts
+++ b/packages/cli/src/create/bin.ts
@@ -1300,14 +1300,15 @@ Use \`vp create --list\` to list all available templates, or run \`vp create --h
   // migrate before the vite-plus rewrite so the generated .oxlintrc/.oxfmtrc
   // get merged into vite.config.ts — matching `vp migrate`. Pin the
   // packageManager field (vite_install hardcodes pnpm in CI/non-TTY when no
-  // signal is present) and force yarn's classic node_modules layout
-  // (Plug'n'Play zip entries break @oxlint/migrate's fileURLToPath resolution).
+  // signal is present) and force yarn's pnpm linker (its node_modules entries
+  // are real on-disk files, unlike Plug'n'Play zip entries that break
+  // @oxlint/migrate's fileURLToPath resolution).
   const installAndMigrate = async (installCwd: string) => {
     setPackageManager(fullPath, workspaceInfo.downloadPackageManager);
     if (workspaceInfo.packageManager === PackageManager.yarn) {
       const yarnrcPath = path.join(fullPath, '.yarnrc.yml');
       if (!fs.existsSync(yarnrcPath)) {
-        fs.writeFileSync(yarnrcPath, 'nodeLinker: node-modules\n');
+        fs.writeFileSync(yarnrcPath, 'nodeLinker: pnpm\n');
       }
     }
     updateCreateProgress('Installing dependencies');
diff --git a/packages/cli/src/migration/__tests__/migrator.spec.ts b/packages/cli/src/migration/__tests__/migrator.spec.ts
index 3963fc91bc..1d68acb150 100644
--- a/packages/cli/src/migration/__tests__/migrator.spec.ts
+++ b/packages/cli/src/migration/__tests__/migrator.spec.ts
@@ -1340,7 +1340,7 @@ describe('ensureVitePlusBootstrap', () => {
       nodeLinker: string;
       catalog: Record<string, string>;
     };
-    expect(yarnrc.nodeLinker).toBe('node-modules');
+    expect(yarnrc.nodeLinker).toBe('pnpm');
     expect(yarnrc.catalog.vite).toBe('npm:@voidzero-dev/vite-plus-core@latest');
     expect(yarnrc.catalog.vitest).toBe('npm:@voidzero-dev/vite-plus-test@latest');
     expect(yarnrc.catalog['vite-plus']).toBe('latest');
@@ -1723,7 +1723,7 @@ describe('rewriteMonorepo yarn catalog', () => {
       nodeLinker: string;
       catalogs: Record<string, Record<string, string>>;
     };
-    expect(yarnrc.nodeLinker).toBe('node-modules');
+    expect(yarnrc.nodeLinker).toBe('pnpm');
     expect(yarnrc.catalogs.vite7.vite).toBe('npm:@voidzero-dev/vite-plus-core@latest');
     expect(yarnrc.catalogs.vite7.react).toBe('^18.0.0');
     expect(yarnrc.catalogs.test.vitest).toBe('npm:@voidzero-dev/vite-plus-test@latest');
diff --git a/packages/cli/src/migration/migrator.ts b/packages/cli/src/migration/migrator.ts
index e6950b80da..c483944b5a 100644
--- a/packages/cli/src/migration/migrator.ts
+++ b/packages/cli/src/migration/migrator.ts
@@ -1525,7 +1525,7 @@ function rewriteYarnrcYml(projectPath: string): void {
 
   editYamlFile(yarnrcYmlPath, (doc) => {
     if (!doc.has('nodeLinker')) {
-      doc.set('nodeLinker', 'node-modules');
+      doc.set('nodeLinker', 'pnpm');
     }
     // catalog
     rewriteCatalog(doc);
diff --git a/packages/cli/templates/monorepo/_yarnrc.yml b/packages/cli/templates/monorepo/_yarnrc.yml
index 3f2226d6f8..f15ef0bf9b 100644
--- a/packages/cli/templates/monorepo/_yarnrc.yml
+++ b/packages/cli/templates/monorepo/_yarnrc.yml
@@ -1,4 +1,4 @@
-nodeLinker: node-modules
+nodeLinker: pnpm
 catalog:
   '@types/node': ^24
   typescript: ^5
diff --git a/rfcs/migration-command.md b/rfcs/migration-command.md
index db14eacfee..ccb1839161 100644
--- a/rfcs/migration-command.md
+++ b/rfcs/migration-command.md
@@ -547,11 +547,14 @@ peerDependencyRules:
 `.yarnrc.yml`
 
 ```yaml
+nodeLinker: pnpm
 catalog:
   vite: npm:@voidzero-dev/vite-plus-core@latest
   vitest: npm:@voidzero-dev/vite-plus-test@latest
 ```
 
+`nodeLinker` is only added when absent, so a project that already pins a linker keeps its own value. The `pnpm` linker is used (real on-disk `node_modules` entries via a content-addressable store) rather than yarn's default Plug'n'Play, whose zip entries break `@oxlint/migrate`'s `fileURLToPath` resolution.
+
 `package.json`
 
 ```json