diff --git a/packages/core/src/loader/file_loader.ts b/packages/core/src/loader/file_loader.ts
index afb9e664e9..9a55d1e8b0 100644
--- a/packages/core/src/loader/file_loader.ts
+++ b/packages/core/src/loader/file_loader.ts
@@ -92,6 +92,10 @@ export class FileLoader {
   constructor(options: FileLoaderOptions) {
     assert(options.directory, 'options.directory is required');
     assert(options.target, 'options.target is required');
+    // Auto-resolve manifest from inject (the app) when not explicitly provided
+    if (!options.manifest && options.inject) {
+      options.manifest = options.inject.loader?.manifest;
+    }
     this.options = {
       caseStyle: CaseStyle.camel,
       call: true,
diff --git a/packages/core/test/loader/manifest_coverage.test.ts b/packages/core/test/loader/manifest_coverage.test.ts
new file mode 100644
index 0000000000..7b8cec42e8
--- /dev/null
+++ b/packages/core/test/loader/manifest_coverage.test.ts
@@ -0,0 +1,103 @@
+import assert from 'node:assert/strict';
+import path from 'node:path';
+
+import { describe, it, afterAll } from 'vitest';
+
+import { createApp, getFilepath, type Application } from '../helper.js';
+
+describe('ManifestStore coverage: FileLoader getter auto-injects manifest', () => {
+  let app: Application;
+
+  afterAll(() => app?.close());
+
+  it('should collect fileDiscovery when plugin uses app.loader.FileLoader', async () => {
+    app = createApp('middleware-override');
+    await app.loader.loadPlugin();
+    await app.loader.loadConfig();
+    await app.loader.loadCustomApp();
+    await app.loader.loadMiddleware();
+    await app.loader.loadController();
+    await app.loader.loadRouter();
+
+    const manifest = app.loader.generateManifest();
+
+    // resolveCache should contain resolved files (extend files, router, configs, boot hooks)
+    assert.ok(Object.keys(manifest.resolveCache).length > 0, 'resolveCache should have entries');
+
+    // fileDiscovery should contain directory scans from middleware, controller loading
+    assert.ok(Object.keys(manifest.fileDiscovery).length > 0, 'fileDiscovery should have entries');
+
+    // All resolveCache keys should be relative paths
+    for (const key of Object.keys(manifest.resolveCache)) {
+      assert.ok(!path.isAbsolute(key), `resolveCache key should be relative: ${key}`);
+      const value = manifest.resolveCache[key];
+      if (value !== null) {
+        assert.ok(!path.isAbsolute(value), `resolveCache value should be relative: ${value}`);
+      }
+    }
+
+    // All fileDiscovery keys should be relative paths
+    for (const key of Object.keys(manifest.fileDiscovery)) {
+      assert.ok(!path.isAbsolute(key), `fileDiscovery key should be relative: ${key}`);
+    }
+  });
+
+  it('should auto-inject manifest into FileLoader created via app.loader.FileLoader', async () => {
+    const testApp = createApp('context-loader');
+    await testApp.loader.loadPlugin();
+    await testApp.loader.loadConfig();
+    await testApp.loader.loadCustomApp();
+
+    // Use app.loader.FileLoader (the getter) to create a loader like plugins do
+    const CustomLoader = testApp.loader.FileLoader;
+    const target = {};
+    const directory = getFilepath('context-loader/app/service');
+    const loader = new CustomLoader({
+      directory,
+      target,
+      inject: testApp,
+    });
+    await loader.load();
+
+    // Generate manifest and verify fileDiscovery captured the directory scan
+    const manifest = testApp.loader.generateManifest();
+    const relDir = path.relative(testApp.loader.options.baseDir, directory).replaceAll(path.sep, '/');
+
+    assert.ok(
+      relDir in manifest.fileDiscovery,
+      `fileDiscovery should contain '${relDir}', got keys: ${Object.keys(manifest.fileDiscovery).join(', ')}`,
+    );
+    assert.ok(Array.isArray(manifest.fileDiscovery[relDir]));
+    assert.ok(manifest.fileDiscovery[relDir].length > 0, 'fileDiscovery should have files');
+
+    await testApp.close();
+  });
+
+  it('should auto-inject manifest into ContextLoader created via app.loader.ContextLoader', async () => {
+    const testApp = createApp('context-loader');
+    await testApp.loader.loadPlugin();
+    await testApp.loader.loadConfig();
+    await testApp.loader.loadCustomApp();
+
+    // Use app.loader.ContextLoader (the getter)
+    const CustomContextLoader = testApp.loader.ContextLoader;
+    const directory = getFilepath('context-loader/app/service');
+    const loader = new CustomContextLoader({
+      directory,
+      property: 'testService',
+      inject: testApp,
+    });
+    await loader.load();
+
+    // Generate manifest and verify fileDiscovery captured the directory scan
+    const manifest = testApp.loader.generateManifest();
+    const relDir = path.relative(testApp.loader.options.baseDir, directory).replaceAll(path.sep, '/');
+
+    assert.ok(
+      relDir in manifest.fileDiscovery,
+      `fileDiscovery should contain '${relDir}', got keys: ${Object.keys(manifest.fileDiscovery).join(', ')}`,
+    );
+
+    await testApp.close();
+  });
+});