diff --git a/tooling/check-repository.mjs b/tooling/check-repository.mjs
index bcd1271..4e11513 100644
--- a/tooling/check-repository.mjs
+++ b/tooling/check-repository.mjs
@@ -139,6 +139,7 @@ export async function checkRepository(repositoryRoot = defaultRoot, options = {}
   for (const loaderPath of nativeLoaderLockPaths) {
     const loader = rootLock.packages[loaderPath];
     if (!loader) continue;
+    let nativeBindingCount = 0;
     for (const [packageName, version] of Object.entries(
       loader.optionalDependencies ?? {},
     )) {
@@ -151,7 +152,8 @@ export async function checkRepository(repositoryRoot = defaultRoot, options = {}
       const rootPath = `node_modules/${packageName}`;
       const dependencyPath = rootLock.packages[nestedPath] ? nestedPath : rootPath;
       const dependency = rootLock.packages[dependencyPath];
-      assert(dependency, `${loaderPath}: native binding missing: ${packageName}`);
+      if (!dependency) continue;
+      nativeBindingCount += 1;
       assert(
         dependency.version === version,
         `${loaderPath}: native binding version drift: ${packageName}`,
@@ -161,6 +163,7 @@ export async function checkRepository(repositoryRoot = defaultRoot, options = {}
         `${loaderPath}: native binding provenance missing: ${packageName}`,
       );
     }
+    assert(nativeBindingCount > 0, `${loaderPath}: native bindings missing`);
   }
   assert(
     !(await stat(resolve(root, "plugins/design-loop")).catch(() => null)),
diff --git a/tooling/scaffold-smoke.mjs b/tooling/scaffold-smoke.mjs
index 9706318..5c1f60b 100644
--- a/tooling/scaffold-smoke.mjs
+++ b/tooling/scaffold-smoke.mjs
@@ -308,6 +308,31 @@ try {
     expectedScreenshot: screenshot,
   });
   await checkRepository(fixtureRoot);
+
+  const fixtureLockPath = resolve(fixtureRoot, "package-lock.json");
+  const fixtureLockRaw = await readFile(fixtureLockPath, "utf8");
+  const fixtureLock = JSON.parse(fixtureLockRaw);
+  const rolldownPath = "node_modules/rolldown";
+  const rolldownBindings = Object.keys(
+    fixtureLock.packages[rolldownPath]?.optionalDependencies ?? {},
+  ).filter((packageName) => fixtureLock.packages[`node_modules/${packageName}`]);
+  assert.ok(
+    rolldownBindings.length > 1,
+    "fixture must install multiple Rolldown binding lock entries",
+  );
+  delete fixtureLock.packages[`node_modules/${rolldownBindings[0]}`];
+  await writeFile(fixtureLockPath, `${JSON.stringify(fixtureLock, null, 2)}\n`);
+  await checkRepository(fixtureRoot);
+
+  for (const packageName of rolldownBindings.slice(1)) {
+    delete fixtureLock.packages[`node_modules/${packageName}`];
+  }
+  await writeFile(fixtureLockPath, `${JSON.stringify(fixtureLock, null, 2)}\n`);
+  await assert.rejects(
+    checkRepository(fixtureRoot),
+    /node_modules\/rolldown: native bindings missing/,
+  );
+  await writeFile(fixtureLockPath, fixtureLockRaw);
   console.log("plugin scaffold smoke test passed after clean npm ci");
 } finally {
   await rm(fixtureRoot, { recursive: true, force: true });