diff --git a/.yarn/versions/dafa68fb.yml b/.yarn/versions/dafa68fb.yml
new file mode 100644
index 000000000000..3e27c141ce1b
--- /dev/null
+++ b/.yarn/versions/dafa68fb.yml
@@ -0,0 +1,23 @@
+releases:
+  "@yarnpkg/cli": patch
+  "@yarnpkg/plugin-pnpm": patch
+
+declined:
+  - "@yarnpkg/plugin-compat"
+  - "@yarnpkg/plugin-constraints"
+  - "@yarnpkg/plugin-dlx"
+  - "@yarnpkg/plugin-essentials"
+  - "@yarnpkg/plugin-init"
+  - "@yarnpkg/plugin-interactive-tools"
+  - "@yarnpkg/plugin-nm"
+  - "@yarnpkg/plugin-npm-cli"
+  - "@yarnpkg/plugin-pack"
+  - "@yarnpkg/plugin-patch"
+  - "@yarnpkg/plugin-pnp"
+  - "@yarnpkg/plugin-stage"
+  - "@yarnpkg/plugin-typescript"
+  - "@yarnpkg/plugin-version"
+  - "@yarnpkg/plugin-workspace-tools"
+  - "@yarnpkg/builder"
+  - "@yarnpkg/core"
+  - "@yarnpkg/doctor"
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5b54b55bb351..19b34b2a2f54 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,9 @@ Yarn now accepts sponsorships! Please give a look at our [OpenCollective](https:
 
 ## Master
 
+### Installs
+- The pnpm linker no longer tries to remove `node_modules` directory, when `node-modules` linker is active
+
 **Note:** features in `master` can be tried out by running `yarn set version from sources` in your project (existing contrib plugins are updated automatically, while new contrib plugins can be added by running `yarn plugin import from sources <name>`).
 
 ## 3.2.0
diff --git a/packages/plugin-pnpm/sources/PnpmLinker.ts b/packages/plugin-pnpm/sources/PnpmLinker.ts
index 96914f1b4091..8f28458eb9cc 100644
--- a/packages/plugin-pnpm/sources/PnpmLinker.ts
+++ b/packages/plugin-pnpm/sources/PnpmLinker.ts
@@ -274,10 +274,11 @@ class PnpmInstaller implements Installer {
     }
 
     // Wait for the package installs to catch up
-    await this.asyncActions.wait(),
+    await this.asyncActions.wait();
 
     await removeIfEmpty(storeLocation);
-    await removeIfEmpty(getNodeModulesLocation(this.opts.project));
+    if (this.opts.project.configuration.get(`nodeLinker`) !== `node-modules`)
+      await removeIfEmpty(getNodeModulesLocation(this.opts.project));
 
     return {
       customData: this.customData,