diff --git a/scripts/stage-bundled-plugin-runtime-deps.mjs b/scripts/stage-bundled-plugin-runtime-deps.mjs
index 1431bce8fc68b..310cf004fe275 100644
--- a/scripts/stage-bundled-plugin-runtime-deps.mjs
+++ b/scripts/stage-bundled-plugin-runtime-deps.mjs
@@ -489,6 +489,29 @@ function pruneDependencyFilesBySuffixes(depRoot, suffixes) {
   });
 }
 
+function pruneNodeModulesBinDirectories(nodeModulesDir) {
+  if (!fs.existsSync(nodeModulesDir)) {
+    return;
+  }
+  const pending = [nodeModulesDir];
+  while (pending.length > 0) {
+    const currentDir = pending.pop();
+    if (!fs.existsSync(currentDir)) {
+      continue;
+    }
+    for (const entry of fs.readdirSync(currentDir, { withFileTypes: true })) {
+      const entryPath = path.join(currentDir, entry.name);
+      if (entry.name === ".bin") {
+        removePathIfExists(entryPath);
+        continue;
+      }
+      if (entry.isDirectory()) {
+        pending.push(entryPath);
+      }
+    }
+  }
+}
+
 function pruneStagedInstalledDependencyCargo(nodeModulesDir, depName, pruneConfig) {
   const depRoot = dependencyNodeModulesPath(nodeModulesDir, depName);
   if (depRoot === null) {
@@ -526,6 +549,7 @@ function listInstalledDependencyNames(nodeModulesDir) {
 }
 
 function pruneStagedRuntimeDependencyCargo(nodeModulesDir, pruneConfig) {
+  pruneNodeModulesBinDirectories(nodeModulesDir);
   for (const depName of listInstalledDependencyNames(nodeModulesDir)) {
     pruneStagedInstalledDependencyCargo(nodeModulesDir, depName, pruneConfig);
   }
diff --git a/test/scripts/stage-bundled-plugin-runtime-deps.test.ts b/test/scripts/stage-bundled-plugin-runtime-deps.test.ts
index ae6d5b6b2bc9b..153968ec289c3 100644
--- a/test/scripts/stage-bundled-plugin-runtime-deps.test.ts
+++ b/test/scripts/stage-bundled-plugin-runtime-deps.test.ts
@@ -771,8 +771,14 @@ describe("stageBundledPluginRuntimeDeps", () => {
     fs.writeFileSync(path.join(gifwrapDir, "test", "fixtures", "large.gif"), "fixture\n", "utf8");
     const playwrightDir = writePackage("playwright-core");
     fs.mkdirSync(path.join(playwrightDir, "types"), { recursive: true });
+    fs.mkdirSync(path.join(rootNodeModules, ".bin"), { recursive: true });
     fs.writeFileSync(path.join(playwrightDir, "types", "types.d.ts"), "export {};\n", "utf8");
     fs.writeFileSync(path.join(playwrightDir, "index.js"), "export {};\n", "utf8");
+    fs.writeFileSync(path.join(playwrightDir, "cli.js"), "export {};\n", "utf8");
+    fs.symlinkSync(
+      path.join("..", "playwright-core", "cli.js"),
+      path.join(rootNodeModules, ".bin", "playwright-core"),
+    );
     const jimpDir = writePackage("@jimp/plugin-blit");
     fs.mkdirSync(path.join(jimpDir, "src", "__image_snapshots__"), { recursive: true });
     fs.writeFileSync(
@@ -794,6 +800,7 @@ describe("stageBundledPluginRuntimeDeps", () => {
     expect(fs.existsSync(path.join(pluginDir, "node_modules", "playwright-core", "index.js"))).toBe(
       true,
     );
+    expect(fs.existsSync(path.join(pluginDir, "node_modules", ".bin"))).toBe(false);
     expect(
       fs.existsSync(
         path.join(pluginDir, "node_modules", "@jimp", "plugin-blit", "src", "__image_snapshots__"),