diff --git a/.github/actions/install-dependencies/action.yml b/.github/actions/install-dependencies/action.yml
index 420b26b59d49..27971a484f63 100644
--- a/.github/actions/install-dependencies/action.yml
+++ b/.github/actions/install-dependencies/action.yml
@@ -23,6 +23,39 @@ runs:
     - name: Install pnpm
       uses: ./.github/actions/install-pnpm
 
+    # When the node_modules layout changes, `pnpm install` keeps the `.bin` scripts of the workspace packages, which
+    # then point into a folder that the new layout does not have. Branches that change `nodeLinker` share this cache
+    # volume, so start from empty node_modules folders when the layout on the volume differs, or when an earlier
+    # install already left such broken `.bin` scripts behind.
+    - name: Remove node_modules of another layout
+      run: |
+        mapfile -t dirs < <(grep '/node_modules$' <<< "$DEPENDENCY_PATHS")
+        expected=$(pnpm config get node-linker)
+        if [[ "$expected" == undefined ]]; then
+          expected=isolated
+        fi
+        actual=$(node -p 'try { JSON.parse(require("fs").readFileSync("node_modules/.modules.yaml", "utf8")).nodeLinker ?? "" } catch { "" }')
+        if [[ -n "$actual" && "$actual" != "$expected" ]]; then
+          reason="The node_modules folders use the $actual layout, but nodeLinker is $expected."
+        else
+          broken=$(node "$GITHUB_ACTION_PATH/find-broken-bin.mjs" "${dirs[@]}")
+          if [[ -n "$broken" ]]; then
+            reason="The target of $broken does not exist."
+          fi
+        fi
+        if [[ -n "$reason" ]]; then
+          echo "$reason Removing the node_modules folders."
+          for dir in "${dirs[@]}"; do
+            if [[ -d "$dir" ]]; then
+              # The folders are mounted from the cache volume, so empty them instead of removing them
+              find "$dir/" -mindepth 1 -maxdepth 1 -exec rm -rf {} +
+            fi
+          done
+        fi
+      env:
+        DEPENDENCY_PATHS: ${{ steps.paths.outputs.paths }}
+      shell: bash
+
     # The cache volume can hold node_modules of another commit or branch. This is a no-op when they match
     # pnpm-lock.yaml.
     - name: Install dependencies
diff --git a/.github/actions/install-dependencies/find-broken-bin.mjs b/.github/actions/install-dependencies/find-broken-bin.mjs
new file mode 100644
index 000000000000..24aa8753cac5
--- /dev/null
+++ b/.github/actions/install-dependencies/find-broken-bin.mjs
@@ -0,0 +1,34 @@
+// Prints the first `.bin` entry in the given node_modules folders whose target does not exist.
+import { existsSync, lstatSync, readdirSync, readFileSync } from 'node:fs';
+import { join, resolve } from 'node:path';
+
+// The pnpm shell shim runs the target with `exec <node> "$basedir_abs/<path>"` (`$basedir` in older versions)
+const SHIM_TARGET = /^\s*exec \S+\s+"\$basedir(?:_abs)?\/([^"]+)"/m;
+
+for (const dir of process.argv.slice(2)) {
+  const binDir = join(dir, '.bin');
+  let names;
+  try {
+    names = readdirSync(binDir);
+  } catch {
+    continue;
+  }
+
+  for (const name of names) {
+    const bin = join(binDir, name);
+    const stat = lstatSync(bin);
+    let target;
+    if (stat.isSymbolicLink()) {
+      target = bin;
+    } else if (stat.isFile() && stat.size < 64 * 1024) {
+      const match = readFileSync(bin, 'utf8').match(SHIM_TARGET);
+      target = match && resolve(binDir, match[1]);
+    }
+
+    if (target && !existsSync(target)) {
+      // eslint-disable-next-line no-console
+      console.log(bin);
+      process.exit(0);
+    }
+  }
+}