diff --git a/test/test-installation-components.js b/test/test-installation-components.js
index fd3a854ba..0b977884f 100644
--- a/test/test-installation-components.js
+++ b/test/test-installation-components.js
@@ -1722,6 +1722,21 @@ async function runTests() {
     const rescannedModules29 = await generator29.scanInstalledModules(tempFixture29);
     assert(rescannedModules29.includes('agent-only-mod'), 'scanInstalledModules recognizes native-agent-only module');
 
+    // Test scanInstalledModules recognizes multi-entry manifests keyed under SKILL.md
+    const multiEntryModDir29 = path.join(tempFixture29, 'multi-entry-mod');
+    await fs.ensureDir(path.join(multiEntryModDir29, 'deep', 'nested', 'bmad-tea'));
+    await fs.writeFile(
+      path.join(multiEntryModDir29, 'deep', 'nested', 'bmad-tea', 'bmad-skill-manifest.yaml'),
+      'SKILL.md:\n  type: agent\n  canonicalId: bmad-tea\n',
+    );
+    await fs.writeFile(
+      path.join(multiEntryModDir29, 'deep', 'nested', 'bmad-tea', 'SKILL.md'),
+      '---\nname: bmad-tea\ndescription: desc\n---\n\nAgent menu.\n',
+    );
+
+    const rescannedModules29b = await generator29.scanInstalledModules(tempFixture29);
+    assert(rescannedModules29b.includes('multi-entry-mod'), 'scanInstalledModules recognizes multi-entry native-agent module');
+
     // skill-manifest.csv should include the native agent entrypoint
     const skillManifestCsv29 = await fs.readFile(path.join(tempFixture29, '_config', 'skill-manifest.csv'), 'utf8');
     assert(skillManifestCsv29.includes('bmad-tea'), 'skill-manifest.csv includes native type:agent SKILL.md entrypoint');
diff --git a/tools/cli/installers/lib/core/manifest-generator.js b/tools/cli/installers/lib/core/manifest-generator.js
index 7932f1516..c9b85db27 100644
--- a/tools/cli/installers/lib/core/manifest-generator.js
+++ b/tools/cli/installers/lib/core/manifest-generator.js
@@ -60,6 +60,19 @@ class ManifestGenerator {
     return artifactType === 'skill' || artifactType === 'agent';
   }
 
+  /**
+   * Check whether a loaded bmad-skill-manifest.yaml declares a native
+   * SKILL.md entrypoint, either as a single-entry manifest or a multi-entry map.
+   * @param {Object|null} manifest - Loaded manifest
+   * @returns {boolean} True when the manifest contains a native skill/agent entrypoint
+   */
+  hasNativeSkillManifest(manifest) {
+    if (!manifest) return false;
+    if (manifest.__single) return this.isNativeSkillDirType(manifest.__single.type);
+
+    return Object.values(manifest).some((entry) => this.isNativeSkillDirType(entry?.type));
+  }
+
   /**
    * Clean text for CSV output by normalizing whitespace.
    * Note: Quote escaping is handled by escapeCsv() at write time.
@@ -1391,8 +1404,8 @@ class ManifestGenerator {
   }
 
   /**
-   * Recursively check if a directory tree contains a bmad-skill-manifest.yaml with
-   * type: skill or type: agent.
+   * Recursively check if a directory tree contains a bmad-skill-manifest.yaml that
+   * declares a native SKILL.md entrypoint (type: skill or type: agent).
    * Skips directories starting with . or _.
    * @param {string} dir - Directory to search
    * @returns {boolean} True if a skill manifest is found
@@ -1407,10 +1420,7 @@ class ManifestGenerator {
 
     // Check for manifest in this directory
     const manifest = await this.loadSkillManifest(dir);
-    if (manifest) {
-      const type = this.getArtifactType(manifest, 'workflow.md');
-      if (this.isNativeSkillDirType(type)) return true;
-    }
+    if (this.hasNativeSkillManifest(manifest)) return true;
 
     // Recurse into subdirectories
     for (const entry of entries) {