diff --git a/src/resources/extensions/gsd/doctor-environment.ts b/src/resources/extensions/gsd/doctor-environment.ts
index 17a266ce8..563afdbb4 100644
--- a/src/resources/extensions/gsd/doctor-environment.ts
+++ b/src/resources/extensions/gsd/doctor-environment.ts
@@ -149,21 +149,44 @@ function checkDependenciesInstalled(basePath: string): EnvironmentCheckResult |
     };
   }
 
-  // Check if lockfile is newer than node_modules
-  const lockfiles = ["package-lock.json", "yarn.lock", "pnpm-lock.yaml"];
-  for (const lockfile of lockfiles) {
-    const lockPath = join(basePath, lockfile);
+  // Check if lockfile is newer than the last install.
+  //
+  // Each package manager writes a metadata marker inside node_modules on
+  // every install. Comparing the lockfile mtime against the marker is
+  // reliable; comparing against the node_modules *directory* mtime is not,
+  // because directory mtime only changes when entries are added or removed
+  // — not when files inside it are updated. (#1974)
+  const lockfiles: Array<{ lock: string; markers: string[] }> = [
+    { lock: "package-lock.json", markers: ["node_modules/.package-lock.json"] },
+    { lock: "yarn.lock",         markers: ["node_modules/.yarn-integrity"] },
+    { lock: "pnpm-lock.yaml",    markers: ["node_modules/.modules.yaml"] },
+  ];
+
+  for (const { lock, markers } of lockfiles) {
+    const lockPath = join(basePath, lock);
     if (!existsSync(lockPath)) continue;
 
     try {
       const lockMtime = statSync(lockPath).mtimeMs;
-      const nmMtime = statSync(nodeModules).mtimeMs;
 
-      if (lockMtime > nmMtime) {
+      // Prefer the package manager's marker file; fall back to directory mtime
+      // only when no marker exists (e.g., manually created node_modules).
+      let installMtime = 0;
+      for (const marker of markers) {
+        const markerPath = join(basePath, marker);
+        if (existsSync(markerPath)) {
+          installMtime = Math.max(installMtime, statSync(markerPath).mtimeMs);
+        }
+      }
+      if (installMtime === 0) {
+        installMtime = statSync(nodeModules).mtimeMs;
+      }
+
+      if (lockMtime > installMtime) {
         return {
           name: "dependencies",
           status: "warning",
-          message: `${lockfile} is newer than node_modules — dependencies may be stale`,
+          message: `${lock} is newer than node_modules — dependencies may be stale`,
           detail: `Run npm install / yarn / pnpm install to update`,
         };
       }
diff --git a/src/resources/extensions/gsd/tests/doctor-environment.test.ts b/src/resources/extensions/gsd/tests/doctor-environment.test.ts
index 35dfc52e9..59263f2b7 100644
--- a/src/resources/extensions/gsd/tests/doctor-environment.test.ts
+++ b/src/resources/extensions/gsd/tests/doctor-environment.test.ts
@@ -15,7 +15,7 @@ import assert from 'node:assert/strict';
  *   - Report formatting
  */
 
-import { mkdtempSync, mkdirSync, writeFileSync, rmSync } from "node:fs";
+import { mkdtempSync, mkdirSync, writeFileSync, rmSync, utimesSync } from "node:fs";
 import { join, dirname } from "node:path";
 import { tmpdir } from "node:os";
 
@@ -102,6 +102,120 @@ describe('doctor-environment', async () => {
       assert.deepStrictEqual(depsCheck!.status, "ok", "existing node_modules is ok");
     });
 
+    // ── Stale Dependencies: marker file check (#1974) ──────────────────
+    console.log("\n=== env: npm marker file newer than lockfile → ok (#1974) ===");
+    {
+      // Simulate the exact bug scenario:
+      // 1. node_modules dir mtime is old (no entries added/removed recently)
+      // 2. package-lock.json mtime is recent (npm rewrote it)
+      // 3. node_modules/.package-lock.json mtime is between dir and lockfile
+      //    (npm wrote it during the same install that rewrote the lockfile)
+      //
+      // The bug: code compares lockfile mtime vs dir mtime → false positive warning
+      // The fix: compare lockfile mtime vs marker file mtime → correctly ok
+      const dir = createProjectDir({
+        "package.json": JSON.stringify({ name: "test" }),
+      });
+      mkdirSync(join(dir, "node_modules"), { recursive: true });
+
+      // Simulate the exact bug: npm install with "up to date" rewrites the
+      // lockfile and the marker, but no packages are added/removed so the
+      // directory mtime should be old. We write the marker first (which
+      // bumps dir mtime), then force the dir mtime back to the past.
+      //
+      // Timeline: dir(T-120s) < lockfile(T-5s) ≈ marker(T-5s)
+      // Bug: code compares lockfile vs dir → false positive stale warning
+      // Fix: code compares lockfile vs marker → correctly reports ok
+      const dirTime = new Date(Date.now() - 120_000);
+      const installTime = new Date(Date.now() - 5_000);
+
+      // Write marker file (this bumps dir mtime as a side effect)
+      writeFileSync(join(dir, "node_modules", ".package-lock.json"), "{}");
+      utimesSync(join(dir, "node_modules", ".package-lock.json"), installTime, installTime);
+
+      // Force dir mtime back to the past — simulates no top-level entries changed
+      utimesSync(join(dir, "node_modules"), dirTime, dirTime);
+
+      // Lockfile written at install time (same as marker, or slightly after)
+      writeFileSync(join(dir, "package-lock.json"), "{}");
+      utimesSync(join(dir, "package-lock.json"), installTime, installTime);
+
+      cleanups.push(dir);
+      const results = runEnvironmentChecks(dir);
+      const depsCheck = results.find(r => r.name === "dependencies");
+      assertTrue(depsCheck !== undefined, "dependencies check runs");
+      assertEq(depsCheck!.status, "ok", "npm marker newer than lockfile → not stale");
+    }
+
+    console.log("\n=== env: yarn marker file newer than lockfile → ok (#1974) ===");
+    {
+      const dir = createProjectDir({
+        "package.json": JSON.stringify({ name: "test" }),
+      });
+      mkdirSync(join(dir, "node_modules"), { recursive: true });
+
+      const dirTime = new Date(Date.now() - 120_000);
+      const installTime = new Date(Date.now() - 5_000);
+
+      writeFileSync(join(dir, "node_modules", ".yarn-integrity"), "{}");
+      utimesSync(join(dir, "node_modules", ".yarn-integrity"), installTime, installTime);
+      utimesSync(join(dir, "node_modules"), dirTime, dirTime);
+
+      writeFileSync(join(dir, "yarn.lock"), "");
+      utimesSync(join(dir, "yarn.lock"), installTime, installTime);
+
+      cleanups.push(dir);
+      const results = runEnvironmentChecks(dir);
+      const depsCheck = results.find(r => r.name === "dependencies");
+      assertTrue(depsCheck !== undefined, "dependencies check runs");
+      assertEq(depsCheck!.status, "ok", "yarn marker newer than lockfile → not stale");
+    }
+
+    console.log("\n=== env: pnpm marker file newer than lockfile → ok (#1974) ===");
+    {
+      const dir = createProjectDir({
+        "package.json": JSON.stringify({ name: "test" }),
+      });
+      mkdirSync(join(dir, "node_modules"), { recursive: true });
+
+      const dirTime = new Date(Date.now() - 120_000);
+      const installTime = new Date(Date.now() - 5_000);
+
+      writeFileSync(join(dir, "node_modules", ".modules.yaml"), "{}");
+      utimesSync(join(dir, "node_modules", ".modules.yaml"), installTime, installTime);
+      utimesSync(join(dir, "node_modules"), dirTime, dirTime);
+
+      writeFileSync(join(dir, "pnpm-lock.yaml"), "");
+      utimesSync(join(dir, "pnpm-lock.yaml"), installTime, installTime);
+
+      cleanups.push(dir);
+      const results = runEnvironmentChecks(dir);
+      const depsCheck = results.find(r => r.name === "dependencies");
+      assertTrue(depsCheck !== undefined, "dependencies check runs");
+      assertEq(depsCheck!.status, "ok", "pnpm marker newer than lockfile → not stale");
+    }
+
+    console.log("\n=== env: no marker file falls back to dir mtime → stale warning (#1974) ===");
+    {
+      // No marker file exists, lockfile newer than dir → should still warn
+      const dir = createProjectDir({
+        "package.json": JSON.stringify({ name: "test" }),
+      });
+      mkdirSync(join(dir, "node_modules"), { recursive: true });
+
+      const past = new Date(Date.now() - 60_000);
+      utimesSync(join(dir, "node_modules"), past, past);
+
+      writeFileSync(join(dir, "package-lock.json"), "{}");
+      // No marker file written — fallback to dir mtime comparison
+
+      cleanups.push(dir);
+      const results = runEnvironmentChecks(dir);
+      const depsCheck = results.find(r => r.name === "dependencies");
+      assertTrue(depsCheck !== undefined, "dependencies check runs");
+      assertEq(depsCheck!.status, "warning", "no marker + lockfile newer → stale warning");
+    }
+
     // ── Env File Check ─────────────────────────────────────────────────
     test('env: .env.example without .env detected', () => {
       const dir = createProjectDir({