diff --git a/src/core/init.ts b/src/core/init.ts
index 95728dc7e..b968e4211 100644
--- a/src/core/init.ts
+++ b/src/core/init.ts
@@ -453,40 +453,47 @@ export class InitCommand {
   // ═══════════════════════════════════════════════════════════
 
   private async createDirectoryStructure(openspecPath: string, extendMode: boolean): Promise<void> {
+    const directories = [
+      openspecPath,
+      path.join(openspecPath, 'specs'),
+      path.join(openspecPath, 'changes'),
+      path.join(openspecPath, 'changes', 'archive'),
+    ];
+
     if (extendMode) {
       // In extend mode, just ensure directories exist without spinner
-      const directories = [
-        openspecPath,
-        path.join(openspecPath, 'specs'),
-        path.join(openspecPath, 'changes'),
-        path.join(openspecPath, 'changes', 'archive'),
-      ];
-
       for (const dir of directories) {
         await FileSystemUtils.createDirectory(dir);
       }
+      await this.writeGitkeepFiles(openspecPath);
       return;
     }
 
     const spinner = this.startSpinner('Creating OpenSpec structure...');
 
-    const directories = [
-      openspecPath,
-      path.join(openspecPath, 'specs'),
-      path.join(openspecPath, 'changes'),
-      path.join(openspecPath, 'changes', 'archive'),
-    ];
-
     for (const dir of directories) {
       await FileSystemUtils.createDirectory(dir);
     }
 
+    await this.writeGitkeepFiles(openspecPath);
+
     spinner.stopAndPersist({
       symbol: PALETTE.white('▌'),
       text: PALETTE.white('OpenSpec structure created'),
     });
   }
 
+  private async writeGitkeepFiles(openspecPath: string): Promise<void> {
+    const emptyDirs = [
+      path.join(openspecPath, 'specs'),
+      path.join(openspecPath, 'changes'),
+      path.join(openspecPath, 'changes', 'archive'),
+    ];
+    for (const dir of emptyDirs) {
+      await FileSystemUtils.writeFile(path.join(dir, '.gitkeep'), '');
+    }
+  }
+
   // ═══════════════════════════════════════════════════════════
   // SKILL & COMMAND GENERATION
   // ═══════════════════════════════════════════════════════════
diff --git a/test/core/init.test.ts b/test/core/init.test.ts
index 6af92aed2..a6e37c0d8 100644
--- a/test/core/init.test.ts
+++ b/test/core/init.test.ts
@@ -65,6 +65,37 @@ describe('InitCommand', () => {
       expect(await directoryExists(path.join(openspecPath, 'changes', 'archive'))).toBe(true);
     });
 
+    it('should create .gitkeep files in empty directories', async () => {
+      const initCommand = new InitCommand({ tools: 'claude', force: true });
+
+      await initCommand.execute(testDir);
+
+      const openspecPath = path.join(testDir, 'openspec');
+      expect(await fileExists(path.join(openspecPath, 'specs', '.gitkeep'))).toBe(true);
+      expect(await fileExists(path.join(openspecPath, 'changes', '.gitkeep'))).toBe(true);
+      expect(await fileExists(path.join(openspecPath, 'changes', 'archive', '.gitkeep'))).toBe(true);
+    });
+
+    it('should create .gitkeep files in extend mode', async () => {
+      const initCommand1 = new InitCommand({ tools: 'claude', force: true });
+      await initCommand1.execute(testDir);
+
+      const openspecPath = path.join(testDir, 'openspec');
+
+      // Remove .gitkeep files to simulate a cloned repo without them
+      await fs.unlink(path.join(openspecPath, 'specs', '.gitkeep'));
+      await fs.unlink(path.join(openspecPath, 'changes', '.gitkeep'));
+      await fs.unlink(path.join(openspecPath, 'changes', 'archive', '.gitkeep'));
+
+      // Re-run init (triggers extend mode since openspec dir already exists)
+      const initCommand2 = new InitCommand({ tools: 'claude', force: true });
+      await initCommand2.execute(testDir);
+
+      expect(await fileExists(path.join(openspecPath, 'specs', '.gitkeep'))).toBe(true);
+      expect(await fileExists(path.join(openspecPath, 'changes', '.gitkeep'))).toBe(true);
+      expect(await fileExists(path.join(openspecPath, 'changes', 'archive', '.gitkeep'))).toBe(true);
+    });
+
     it('should create config.yaml with default schema', async () => {
       const initCommand = new InitCommand({ tools: 'claude', force: true });