diff --git a/scripts/postinstall.js b/scripts/postinstall.js
index 60251501..0da1a18b 100755
--- a/scripts/postinstall.js
+++ b/scripts/postinstall.js
@@ -68,24 +68,13 @@ function validateConfiguration() {
     errors.push('~/.ccs/ directory not found');
   }
 
-  // Check required files (GLM/GLMT/Kimi are now optional - created via presets)
-  const requiredFiles = [
-    { path: path.join(ccsDir, 'config.json'), name: 'config.json' }
-  ];
+  // Check for config file - prefer config.yaml, fallback to config.json
+  const configYaml = path.join(ccsDir, 'config.yaml');
+  const configJson = path.join(ccsDir, 'config.json');
+  const hasConfig = fs.existsSync(configYaml) || fs.existsSync(configJson);
 
-  for (const file of requiredFiles) {
-    if (!fs.existsSync(file.path)) {
-      errors.push(`${file.name} not found`);
-      continue;
-    }
-
-    // Validate JSON syntax
-    try {
-      const content = fs.readFileSync(file.path, 'utf8');
-      JSON.parse(content);
-    } catch (e) {
-      errors.push(`${file.name} has invalid JSON: ${e.message}`);
-    }
+  if (!hasConfig) {
+    errors.push('config.yaml (or config.json) not found');
   }
 
   // Check ~/.claude/settings.json (warning only, not critical)
@@ -150,62 +139,77 @@ function createConfigFiles() {
     // Users can run "ccs sync" to install CCS commands/skills to ~/.claude/
     // This gives users control over when to modify their Claude configuration
 
-    // Create config.json if missing
+    // Create config.yaml if missing (primary format)
     // NOTE: gemini/codex profiles NOT included - they are added on-demand when user
     // runs `ccs gemini` or `ccs codex` for first time (requires OAuth auth first)
     // NOTE: GLM/GLMT/Kimi profiles are now created via UI/CLI presets, not auto-created
-    const configPath = path.join(ccsDir, 'config.json');
-    if (!fs.existsSync(configPath)) {
-      // NOTE: No 'default' entry - when no profile specified, CCS passes through
-      // to Claude's native auth without --settings flag. This prevents env var
-      // pollution from affecting the default profile.
-      // Profiles are empty by default - users create via `ccs api create --preset` or UI
-      const config = {
-        profiles: {}
-      };
+    const configYamlPath = path.join(ccsDir, 'config.yaml');
+    const legacyConfigPath = path.join(ccsDir, 'config.json');
 
-      // Atomic write: temp file → rename
-      const tmpPath = `${configPath}.tmp`;
-      fs.writeFileSync(tmpPath, JSON.stringify(config, null, 2) + '\n', 'utf8');
-      fs.renameSync(tmpPath, configPath);
-
-      console.log('[OK] Created config: ~/.ccs/config.json');
-    } else {
-      // Update existing config (migration for older versions)
-      const config = JSON.parse(fs.readFileSync(configPath, 'utf8'));
-      // Ensure profiles object exists
-      if (!config.profiles) {
-        config.profiles = {};
-      }
-      let configUpdated = false;
-
-      // Migration: Add glmt if missing (v3.x)
-      if (!config.profiles.glmt) {
-        config.profiles.glmt = '~/.ccs/glmt.settings.json';
-        configUpdated = true;
-      }
-
-      // Migration: Remove 'default' entry pointing to ~/.claude/settings.json (v5.4.0)
-      // This entry caused the default profile to pass --settings flag, which could
-      // pick up stale env vars (ANTHROPIC_BASE_URL) from previous profile sessions.
-      // Fix: Let CCS pass through to Claude's native auth without --settings flag.
-      if (config.profiles.default === '~/.claude/settings.json') {
-        delete config.profiles.default;
-        configUpdated = true;
-        console.log('[OK] Removed legacy default profile (now uses native Claude auth)');
-      }
-
-      // NOTE: gemini/codex profiles added on-demand, not during migration
-      if (configUpdated) {
-        const tmpPath = `${configPath}.tmp`;
-        fs.writeFileSync(tmpPath, JSON.stringify(config, null, 2) + '\n', 'utf8');
-        fs.renameSync(tmpPath, configPath);
-        if (!config.profiles.glmt) {
-          console.log('[OK] Updated config with glmt profile');
-        }
+    if (!fs.existsSync(configYamlPath)) {
+      // Check for legacy config.json - autoMigrate() in ccs.ts will handle migration
+      if (fs.existsSync(legacyConfigPath)) {
+        console.log('[OK] Legacy config.json found - will migrate to config.yaml on first run');
       } else {
-        console.log('[OK] Config exists: ~/.ccs/config.json (preserved)');
+        // Try to use unified config loader if dist is available
+        try {
+          const { saveUnifiedConfig } = require('../dist/config/unified-config-loader');
+          const { createEmptyUnifiedConfig, UNIFIED_CONFIG_VERSION } = require('../dist/config/unified-config-types');
+
+          const config = createEmptyUnifiedConfig();
+          config.version = UNIFIED_CONFIG_VERSION;
+          saveUnifiedConfig(config);
+
+          console.log('[OK] Created config: ~/.ccs/config.yaml');
+        } catch (loaderErr) {
+          // Dist not built yet (fresh clone) - create minimal config.yaml manually
+          const yaml = require('js-yaml');
+          const config = {
+            version: '2.0',
+            profiles: {},
+            accounts: {},
+            cliproxy: {
+              variants: {},
+              oauth_accounts: {}
+            },
+            cliproxy_server: {
+              local: {
+                port: 8317,
+                auto_start: true
+              }
+            }
+          };
+
+          try {
+            const yamlContent = yaml.dump(config, {
+              indent: 2,
+              lineWidth: -1,
+              noRefs: true,
+              sortKeys: false
+            });
+            const tmpPath = `${configYamlPath}.tmp`;
+            fs.writeFileSync(tmpPath, yamlContent, 'utf8');
+            fs.renameSync(tmpPath, configYamlPath);
+            console.log('[OK] Created config: ~/.ccs/config.yaml');
+          } catch (yamlErr) {
+            // Final fallback: create legacy config.json
+            console.warn('[!] YAML write failed, creating legacy config.json');
+            const fallbackConfig = { profiles: {} };
+            const tmpPath = `${legacyConfigPath}.tmp`;
+            fs.writeFileSync(tmpPath, JSON.stringify(fallbackConfig, null, 2) + '\n', 'utf8');
+            fs.renameSync(tmpPath, legacyConfigPath);
+            console.log('[OK] Created config: ~/.ccs/config.json (fallback)');
+          }
+        }
       }
+    } else {
+      console.log('[OK] Config exists: ~/.ccs/config.yaml (preserved)');
+    }
+
+    // Handle legacy config.json migrations (for users upgrading)
+    if (fs.existsSync(legacyConfigPath) && !fs.existsSync(configYamlPath)) {
+      // Migration will happen via autoMigrate() in ccs.ts on first run
+      console.log('[i] Legacy config.json will be migrated to config.yaml on first run');
     }
 
     // NOTE: GLM, GLMT, and Kimi profiles are NO LONGER auto-created during install
diff --git a/src/commands/setup-command.ts b/src/commands/setup-command.ts
index ec990812..ff867eaf 100644
--- a/src/commands/setup-command.ts
+++ b/src/commands/setup-command.ts
@@ -93,10 +93,31 @@ async function selectOption(
 }
 
 /**
- * Check if this is a first-time install (no config exists)
+ * Check if this is a first-time install (config exists but is empty/unconfigured)
+ * Returns true if user should be prompted to run setup wizard
  */
 export function isFirstTimeInstall(): boolean {
-  return !hasUnifiedConfig();
+  // No config at all → definitely first time
+  if (!hasUnifiedConfig()) {
+    return true;
+  }
+
+  // Config exists - check if it's meaningfully configured
+  const config = loadOrCreateUnifiedConfig();
+
+  // Check for any meaningful configuration
+  const hasProfiles = Object.keys(config.profiles || {}).length > 0;
+  const hasAccounts = Object.keys(config.accounts || {}).length > 0;
+  const hasVariants = Object.keys(config.cliproxy?.variants || {}).length > 0;
+  const hasOAuthAccounts = Object.keys(config.cliproxy?.oauth_accounts || {}).length > 0;
+  const hasRemoteProxy =
+    config.cliproxy_server?.remote?.enabled && config.cliproxy_server?.remote?.host;
+
+  // If any of these exist, user has configured something
+  const isConfigured =
+    hasProfiles || hasAccounts || hasVariants || hasOAuthAccounts || hasRemoteProxy;
+
+  return !isConfigured;
 }
 
 /**
diff --git a/src/management/recovery-manager.ts b/src/management/recovery-manager.ts
index 9c43dd1e..b93621d3 100644
--- a/src/management/recovery-manager.ts
+++ b/src/management/recovery-manager.ts
@@ -8,6 +8,8 @@ import * as fs from 'fs';
 import * as path from 'path';
 import * as os from 'os';
 import { info } from '../utils/ui';
+import { createEmptyUnifiedConfig, UNIFIED_CONFIG_VERSION } from '../config/unified-config-types';
+import { saveUnifiedConfig, hasUnifiedConfig } from '../config/unified-config-loader';
 
 /**
  * Get CCS home directory (respects CCS_HOME env for test isolation)
@@ -49,37 +51,39 @@ class RecoveryManager {
   }
 
   /**
-   * Ensure ~/.ccs/config.json exists with defaults
+   * Ensure ~/.ccs/config.yaml exists with defaults
+   * This is the primary config format (YAML unified config)
    */
-  ensureConfigJson(): boolean {
-    const configPath = path.join(this.ccsDir, 'config.json');
-
-    // Check if exists and valid
-    if (fs.existsSync(configPath)) {
-      try {
-        const content = fs.readFileSync(configPath, 'utf8');
-        JSON.parse(content); // Validate JSON
-        return false; // No recovery needed
-      } catch (_e) {
-        // Corrupted - backup and recreate
-        const backupPath = `${configPath}.backup.${Date.now()}`;
-        fs.renameSync(configPath, backupPath);
-        this.recovered.push(`Backed up corrupted config.json to ${path.basename(backupPath)}`);
-      }
+  ensureConfigYaml(): boolean {
+    // Skip if config.yaml already exists
+    if (hasUnifiedConfig()) {
+      return false;
     }
 
-    // Create default config (matches postinstall.js)
-    // NOTE: Empty profiles - users create profiles via `ccs api create` or UI
-    const defaultConfig = {
-      profiles: {},
-    };
+    // Check for legacy config.json - if exists, let autoMigrate handle it
+    const legacyConfigPath = path.join(this.ccsDir, 'config.json');
+    if (fs.existsSync(legacyConfigPath)) {
+      // Legacy config exists - autoMigrate() in ccs.ts will handle migration
+      return false;
+    }
 
-    const tmpPath = `${configPath}.tmp`;
-    fs.writeFileSync(tmpPath, JSON.stringify(defaultConfig, null, 2) + '\n', 'utf8');
-    fs.renameSync(tmpPath, configPath);
+    // Create fresh config.yaml with defaults
+    const config = createEmptyUnifiedConfig();
+    config.version = UNIFIED_CONFIG_VERSION;
 
-    this.recovered.push('Created ~/.ccs/config.json');
-    return true;
+    try {
+      saveUnifiedConfig(config);
+      this.recovered.push('Created ~/.ccs/config.yaml');
+      return true;
+    } catch (_e) {
+      // Fallback: create minimal config.json for backward compat
+      const fallbackConfig = { profiles: {} };
+      const tmpPath = `${legacyConfigPath}.tmp`;
+      fs.writeFileSync(tmpPath, JSON.stringify(fallbackConfig, null, 2) + '\n', 'utf8');
+      fs.renameSync(tmpPath, legacyConfigPath);
+      this.recovered.push('Created ~/.ccs/config.json (fallback)');
+      return true;
+    }
   }
 
   /**
@@ -281,8 +285,8 @@ class RecoveryManager {
     this.ensureSharedDirectories();
     this.ensureClaudeSettings();
 
-    // Config files (core only - no GLM/GLMT/Kimi auto-creation)
-    this.ensureConfigJson();
+    // Config files - use YAML as primary format
+    this.ensureConfigYaml();
 
     // Shell completions
     this.ensureShellCompletions();
diff --git a/tests/npm/postinstall.test.js b/tests/npm/postinstall.test.js
index 07572362..136df681 100644
--- a/tests/npm/postinstall.test.js
+++ b/tests/npm/postinstall.test.js
@@ -19,19 +19,25 @@ describe('npm postinstall', () => {
     }
   });
 
-  it('creates config.json', () => {
+  it('creates config.yaml (primary format)', () => {
     execSync(`node "${postinstallScript}"`, {
       stdio: 'ignore',
       env: { ...process.env, CCS_HOME: testEnv.testHome }
     });
 
-    assert(testEnv.fileExists('config.json'), 'config.json should be created');
+    // config.yaml is now the primary format (v6.x+)
+    assert(testEnv.fileExists('config.yaml'), 'config.yaml should be created');
 
-    const config = testEnv.readFile('config.json', true);
-    assert(config.profiles, 'config.json should have profiles');
+    // Read YAML config and verify structure
+    const yaml = require('js-yaml');
+    const configContent = testEnv.readFile('config.yaml', false);
+    const config = yaml.load(configContent);
+
+    assert(config.profiles !== undefined, 'config.yaml should have profiles');
     assert(typeof config.profiles === 'object', 'profiles should be an object');
     // Profiles are now empty by default - users create via presets
     assert.deepStrictEqual(config.profiles, {}, 'profiles should be empty by default');
+    assert(config.version, 'config.yaml should have version');
   });
 
   it('does NOT auto-create glm.settings.json (v6.0 - use presets instead)', () => {
@@ -49,24 +55,30 @@ describe('npm postinstall', () => {
 
   it('is idempotent', () => {
     const env = { ...process.env, CCS_HOME: testEnv.testHome };
+    const yaml = require('js-yaml');
 
     // Run postinstall first time
     execSync(`node "${postinstallScript}"`, { stdio: 'ignore', env });
 
-    // Create custom config
+    // Create custom config.yaml to test preservation
     const customConfig = {
+      version: '2.0',
       profiles: {
         custom: '~/.custom.json',
         glm: '~/.ccs/glm.settings.json'
-      }
+      },
+      accounts: {},
+      cliproxy: { variants: {}, oauth_accounts: {} }
     };
-    testEnv.createFile('config.json', customConfig);
+    const yamlContent = yaml.dump(customConfig, { indent: 2 });
+    testEnv.createFile('config.yaml', yamlContent);
 
     // Run postinstall again
     execSync(`node "${postinstallScript}"`, { stdio: 'ignore', env });
 
     // Verify custom config preserved
-    const config = testEnv.readFile('config.json', true);
+    const configContent = testEnv.readFile('config.yaml', false);
+    const config = yaml.load(configContent);
     assert(config.profiles.custom, 'Custom profile should be preserved');
     assert.strictEqual(config.profiles.custom, '~/.custom.json');
   });
@@ -97,7 +109,7 @@ describe('npm postinstall', () => {
 
     // Verify existing file still exists and new files are created
     assert(testEnv.fileExists('existing.txt'), 'Existing files should be preserved');
-    assert(testEnv.fileExists('config.json'), 'config.json should be created');
+    assert(testEnv.fileExists('config.yaml'), 'config.yaml should be created');
     // GLM/GLMT/Kimi are no longer auto-created
     assert(!testEnv.fileExists('glm.settings.json'), 'glm.settings.json should NOT be auto-created');
   });