diff --git a/packages/cli/src/config/config.ts b/packages/cli/src/config/config.ts
index 0b54b901c..bf9fa5196 100755
--- a/packages/cli/src/config/config.ts
+++ b/packages/cli/src/config/config.ts
@@ -1034,8 +1034,9 @@ export async function loadCliConfig(
       format: outputSettingsFormat,
     },
     hooks: settings.hooks,
+    hooksConfig: settings.hooksConfig,
     enableHooks:
-      argv.experimentalHooks === true || settings.hooks?.enabled === true,
+      argv.experimentalHooks === true || settings.hooksConfig?.enabled === true,
     channel: argv.channel,
     // Precedence: explicit CLI flag > settings file > default(true).
     // NOTE: do NOT set a yargs default for `chat-recording`, otherwise argv will
diff --git a/packages/cli/src/config/settingsSchema.ts b/packages/cli/src/config/settingsSchema.ts
index 9ef11cf4f..73c47a650 100644
--- a/packages/cli/src/config/settingsSchema.ts
+++ b/packages/cli/src/config/settingsSchema.ts
@@ -1177,24 +1177,24 @@ const SETTINGS_SCHEMA = {
     showInDialog: false,
   },
 
-  hooks: {
+  hooksConfig: {
     type: 'object',
-    label: 'Hooks',
+    label: 'Hooks Config',
     category: 'Advanced',
     requiresRestart: false,
     default: {},
     description:
-      'Hook configurations for extending CLI behavior at various lifecycle points.',
+      'Hook configurations for intercepting and customizing agent behavior.',
     showInDialog: false,
     properties: {
       enabled: {
         type: 'boolean',
         label: 'Enable Hooks',
         category: 'Advanced',
-        requiresRestart: false,
-        default: false,
+        requiresRestart: true,
+        default: true,
         description:
-          'Enable the hooks feature. When enabled, hooks defined in UserPromptSubmit and Stop will be executed.',
+          'Canonical toggle for the hooks system. When disabled, no hooks will be executed.',
         showInDialog: false,
       },
       disabled: {
@@ -1204,10 +1204,23 @@ const SETTINGS_SCHEMA = {
         requiresRestart: false,
         default: [] as string[],
         description:
-          'List of hook names to disable. Hooks in this list will not be executed.',
+          'List of hook names (commands) that should be disabled. Hooks in this list will not execute even if configured.',
         showInDialog: false,
         mergeStrategy: MergeStrategy.UNION,
       },
+    },
+  },
+
+  hooks: {
+    type: 'object',
+    label: 'Hooks',
+    category: 'Advanced',
+    requiresRestart: false,
+    default: {},
+    description:
+      'Hook event configurations for extending CLI behavior at various lifecycle points.',
+    showInDialog: false,
+    properties: {
       UserPromptSubmit: {
         type: 'array',
         label: 'Before Agent Hooks',
diff --git a/packages/core/src/config/config.ts b/packages/core/src/config/config.ts
index bf20f1172..61ec4dfe7 100644
--- a/packages/core/src/config/config.ts
+++ b/packages/core/src/config/config.ts
@@ -388,6 +388,8 @@ export interface ConfigParameters {
   enableHooks?: boolean;
   /** Hooks configuration from settings */
   hooks?: Record<string, unknown>;
+  /** Hooks config settings (enabled, disabled list) */
+  hooksConfig?: Record<string, unknown>;
   /** Warnings generated during configuration resolution */
   warnings?: string[];
 }
@@ -532,6 +534,7 @@ export class Config {
   private readonly defaultFileEncoding: FileEncodingType;
   private readonly enableHooks: boolean;
   private readonly hooks?: Record<string, unknown>;
+  private readonly hooksConfig?: Record<string, unknown>;
   private hookSystem?: HookSystem;
   private messageBus?: MessageBus;
 
@@ -690,6 +693,7 @@ export class Config {
     });
     this.enableHooks = params.enableHooks ?? false;
     this.hooks = params.hooks;
+    this.hooksConfig = params.hooksConfig;
   }
 
   /**
@@ -1506,9 +1510,9 @@ export class Config {
    * This is used by the HookRegistry to filter out disabled hooks.
    */
   getDisabledHooks(): string[] {
-    const hooks = this.hooks;
-    if (!hooks) return [];
-    const disabled = hooks['disabled'];
+    const hooksConfig = this.hooksConfig;
+    if (!hooksConfig) return [];
+    const disabled = hooksConfig['disabled'];
     return Array.isArray(disabled) ? (disabled as string[]) : [];
   }