diff --git a/src/commands/doctor/shared/plugin-dependency-cleanup.test.ts b/src/commands/doctor/shared/plugin-dependency-cleanup.test.ts
index baff0db3627..28dcd34d3ba 100644
--- a/src/commands/doctor/shared/plugin-dependency-cleanup.test.ts
+++ b/src/commands/doctor/shared/plugin-dependency-cleanup.test.ts
@@ -29,18 +29,33 @@ describe("cleanupLegacyPluginDependencyState", () => {
       "demo",
       "node_modules",
     );
+    const legacyExtensionStamp = path.join(
+      packageRoot,
+      "dist",
+      "extensions",
+      "demo",
+      ".openclaw-runtime-deps-stamp.json",
+    );
     const legacyManifest = path.join(
       packageRoot,
       "extensions",
       "demo",
       ".openclaw-runtime-deps.json",
     );
+    const thirdPartyNodeModules = path.join(
+      stateDir,
+      "extensions",
+      "lossless-claw",
+      "node_modules",
+    );
 
     await fs.mkdir(legacyRuntimeRoot, { recursive: true });
     await fs.mkdir(legacyLocalRoot, { recursive: true });
     await fs.mkdir(legacyExtensionNodeModules, { recursive: true });
+    await fs.writeFile(legacyExtensionStamp, "{}");
     await fs.mkdir(path.dirname(legacyManifest), { recursive: true });
     await fs.writeFile(legacyManifest, "{}");
+    await fs.mkdir(thirdPartyNodeModules, { recursive: true });
     await fs.mkdir(explicitStageDir, { recursive: true });
     await fs.mkdir(path.join(stateDirectory, "plugin-runtime-deps"), { recursive: true });
 
@@ -55,11 +70,13 @@ describe("cleanupLegacyPluginDependencyState", () => {
         legacyRuntimeRoot,
         legacyLocalRoot,
         legacyExtensionNodeModules,
+        legacyExtensionStamp,
         legacyManifest,
         explicitStageDir,
         path.join(stateDirectory, "plugin-runtime-deps"),
       ]),
     );
+    expect(targets).not.toContain(thirdPartyNodeModules);
 
     const result = await cleanupLegacyPluginDependencyState({ env, packageRoot });
 
@@ -68,7 +85,9 @@ describe("cleanupLegacyPluginDependencyState", () => {
     await expect(fs.stat(legacyRuntimeRoot)).rejects.toThrow();
     await expect(fs.stat(legacyLocalRoot)).rejects.toThrow();
     await expect(fs.stat(legacyExtensionNodeModules)).rejects.toThrow();
+    await expect(fs.stat(legacyExtensionStamp)).rejects.toThrow();
     await expect(fs.stat(legacyManifest)).rejects.toThrow();
+    await expect(fs.stat(thirdPartyNodeModules)).resolves.toBeDefined();
     await expect(fs.stat(explicitStageDir)).rejects.toThrow();
     await expect(fs.stat(path.join(stateDirectory, "plugin-runtime-deps"))).rejects.toThrow();
   });
diff --git a/src/commands/doctor/shared/plugin-dependency-cleanup.ts b/src/commands/doctor/shared/plugin-dependency-cleanup.ts
index e223b258062..652ed274eee 100644
--- a/src/commands/doctor/shared/plugin-dependency-cleanup.ts
+++ b/src/commands/doctor/shared/plugin-dependency-cleanup.ts
@@ -34,14 +34,19 @@ async function pathExists(targetPath: string): Promise<boolean> {
   }
 }
 
-function isLegacyDependencyDebrisName(name: string): boolean {
+function isRuntimeDependencyMarkerName(name: string): boolean {
   return (
-    name === "node_modules" ||
     name === ".openclaw-runtime-deps.json" ||
     name === ".openclaw-runtime-deps-stamp.json" ||
+    name.startsWith(".openclaw-runtime-deps-")
+  );
+}
+
+function isLegacyDependencyDebrisName(name: string): boolean {
+  return (
+    isRuntimeDependencyMarkerName(name) ||
     name === ".openclaw-pnpm-store" ||
     name === ".openclaw-install-backups" ||
-    name.startsWith(".openclaw-runtime-deps-") ||
     name.startsWith(".openclaw-install-stage-")
   );
 }
@@ -59,8 +64,17 @@ async function collectLegacyExtensionDebris(extensionsRoot: string): Promise<str
       continue;
     }
     const pluginRoot = path.join(extensionsRoot, entry.name);
-    for (const childPath of await collectDirectChildren(pluginRoot)) {
-      if (isLegacyDependencyDebrisName(path.basename(childPath))) {
+    const children = await collectDirectChildren(pluginRoot);
+    const hasRuntimeDepsMarker = children.some((childPath) =>
+      isRuntimeDependencyMarkerName(path.basename(childPath)),
+    );
+    for (const childPath of children) {
+      const basename = path.basename(childPath);
+      if (basename === "node_modules" && hasRuntimeDepsMarker) {
+        targets.push(childPath);
+        continue;
+      }
+      if (isLegacyDependencyDebrisName(basename)) {
         targets.push(childPath);
       }
     }