diff --git a/skills-engine/apply.ts b/skills-engine/apply.ts
index 3d5e761..219d025 100644
--- a/skills-engine/apply.ts
+++ b/skills-engine/apply.ts
@@ -5,9 +5,10 @@ import os from 'os';
 import path from 'path';
 
 import { clearBackup, createBackup, restoreBackup } from './backup.js';
-import { NANOCLAW_DIR } from './constants.js';
+import { NANOCLAW_DIR, STATE_FILE } from './constants.js';
 import { copyDir } from './fs-utils.js';
 import { isCustomizeActive } from './customize.js';
+import { initNanoclawDir } from './init.js';
 import { executeFileOps } from './file-ops.js';
 import { acquireLock } from './lock.js';
 import {
@@ -38,7 +39,12 @@ export async function applySkill(skillDir: string): Promise<ApplyResult> {
   const manifest = readManifest(skillDir);
 
   // --- Pre-flight checks ---
-  const currentState = readState(); // Validates state exists and version is compatible
+  // Auto-initialize skills system if state file doesn't exist
+  const statePath = path.join(projectRoot, NANOCLAW_DIR, STATE_FILE);
+  if (!fs.existsSync(statePath)) {
+    initNanoclawDir();
+  }
+  const currentState = readState();
 
   // Check skills system version compatibility
   const sysCheck = checkSystemVersion(manifest);