diff --git a/packages/core/src/config/projectRegistry.test.ts b/packages/core/src/config/projectRegistry.test.ts
index 84d266b278..d3201133a6 100644
--- a/packages/core/src/config/projectRegistry.test.ts
+++ b/packages/core/src/config/projectRegistry.test.ts
@@ -435,4 +435,20 @@ describe('ProjectRegistry', () => {
     expect(data.projects[normalizePath(projectPath)]).toBe('my-project');
     expect(Object.values(data.projects)).not.toContain('../../etc/passwd');
   });
+
+  it('resolves symlinks to the same short ID', async () => {
+    const registry = new ProjectRegistry(registryPath);
+    await registry.initialize();
+
+    const realDir = path.join(tempDir, 'real-project');
+    fs.mkdirSync(realDir);
+
+    const symlinkDir = path.join(tempDir, 'symlink-project');
+    fs.symlinkSync(realDir, symlinkDir, 'dir');
+
+    const id1 = await registry.getShortId(realDir);
+    const id2 = await registry.getShortId(symlinkDir);
+
+    expect(id1).toBe(id2);
+  });
 });
diff --git a/packages/core/src/config/projectRegistry.ts b/packages/core/src/config/projectRegistry.ts
index 88c49ac3af..b50ee61cc2 100644
--- a/packages/core/src/config/projectRegistry.ts
+++ b/packages/core/src/config/projectRegistry.ts
@@ -12,6 +12,7 @@ import { lock } from 'proper-lockfile';
 import { z } from 'zod';
 import { debugLogger } from '../utils/debugLogger.js';
 import { isNodeError } from '../utils/errors.js';
+import { resolveToRealPath } from '../utils/paths.js';
 
 export interface RegistryData {
   projects: Record<string, string>;
@@ -93,7 +94,7 @@ export class ProjectRegistry {
   }
 
   private normalizePath(projectPath: string): string {
-    let resolved = path.resolve(projectPath);
+    let resolved = resolveToRealPath(projectPath);
     if (os.platform() === 'win32') {
       resolved = resolved.toLowerCase();
     }