diff --git a/docs/users/configuration/settings.md b/docs/users/configuration/settings.md
index c814633b7..85902eaf2 100644
--- a/docs/users/configuration/settings.md
+++ b/docs/users/configuration/settings.md
@@ -274,7 +274,6 @@ If you are experiencing performance issues with file searching (e.g., with `@` c
 | `tools.truncateToolOutputThreshold`  | number            | Truncate tool output if it is larger than this many characters. Applies to Shell, Grep, Glob, ReadFile and ReadManyFiles tools.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | `25000`     | Requires restart: Yes                                                                                                                                                                                                                                |
 | `tools.truncateToolOutputLines`      | number            | Maximum lines or entries kept when truncating tool output. Applies to Shell, Grep, Glob, ReadFile and ReadManyFiles tools.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | `1000`      | Requires restart: Yes                                                                                                                                                                                                                                |
 | `tools.autoAccept`                   | boolean           | Controls whether the CLI automatically accepts and executes tool calls that are considered safe (e.g., read-only operations) without explicit user confirmation. If set to `true`, the CLI will bypass the confirmation prompt for tools deemed safe.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                | `false`     |                                                                                                                                                                                                                                                      |
-| `tools.experimental.skills`           | boolean           | Enable experimental Agent Skills feature                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             | `false`     |                                                                                                                                                                                                                                                      |
 
 #### mcp
 
@@ -311,6 +310,12 @@ If you are experiencing performance issues with file searching (e.g., with `@` c
 >
 > **Note about advanced.tavilyApiKey:** This is a legacy configuration format. For Qwen OAuth users, DashScope provider is automatically available without any configuration. For other authentication types, configure Tavily or Google providers using the new `webSearch` configuration format.
 
+#### experimental
+
+| Setting               | Type    | Description                      | Default |
+| --------------------- | ------- | -------------------------------- | ------- |
+| `experimental.skills` | boolean | Enable experimental Agent Skills | `false` |
+
 #### mcpServers
 
 Configures connections to one or more Model-Context Protocol (MCP) servers for discovering and using custom tools. Qwen Code attempts to connect to each configured MCP server to discover available tools. If multiple MCP servers expose a tool with the same name, the tool names will be prefixed with the server alias you defined in the configuration (e.g., `serverAlias__actualToolName`) to avoid conflicts. Note that the system might strip certain schema properties from MCP tool definitions for compatibility. At least one of `command`, `url`, or `httpUrl` must be provided. If multiple are specified, the order of precedence is `httpUrl`, then `url`, then `command`.
diff --git a/packages/cli/src/config/config.ts b/packages/cli/src/config/config.ts
index 74d15522b..818cc0122 100755
--- a/packages/cli/src/config/config.ts
+++ b/packages/cli/src/config/config.ts
@@ -332,7 +332,14 @@ export async function parseArguments(settings: Settings): Promise<CliArgs> {
         .option('experimental-skills', {
           type: 'boolean',
           description: 'Enable experimental Skills feature',
-          default: settings.tools?.experimental?.skills ?? false,
+          default: (() => {
+            const legacySkills = (
+              settings as Settings & {
+                tools?: { experimental?: { skills?: boolean } };
+              }
+            ).tools?.experimental?.skills;
+            return settings.experimental?.skills ?? legacySkills ?? false;
+          })(),
         })
         .option('channel', {
           type: 'string',
diff --git a/packages/cli/src/config/settings.ts b/packages/cli/src/config/settings.ts
index d9e5edb30..9d6e7c8e3 100644
--- a/packages/cli/src/config/settings.ts
+++ b/packages/cli/src/config/settings.ts
@@ -921,6 +921,21 @@ export function migrateDeprecatedSettings(
 
       loadedSettings.setValue(scope, 'extensions', newExtensionsValue);
     }
+
+    const legacySkills = (
+      settings as Settings & {
+        tools?: { experimental?: { skills?: boolean } };
+      }
+    ).tools?.experimental?.skills;
+    if (
+      legacySkills !== undefined &&
+      settings.experimental?.skills === undefined
+    ) {
+      console.log(
+        `Migrating deprecated tools.experimental.skills setting from ${scope} settings...`,
+      );
+      loadedSettings.setValue(scope, 'experimental.skills', legacySkills);
+    }
   };
 
   processScope(SettingScope.User);
diff --git a/packages/cli/src/config/settingsSchema.ts b/packages/cli/src/config/settingsSchema.ts
index 1e72ad48b..cae4d2c66 100644
--- a/packages/cli/src/config/settingsSchema.ts
+++ b/packages/cli/src/config/settingsSchema.ts
@@ -972,27 +972,6 @@ const SETTINGS_SCHEMA = {
         description: 'The number of lines to keep when truncating tool output.',
         showInDialog: true,
       },
-      experimental: {
-        type: 'object',
-        label: 'Experimental',
-        category: 'Tools',
-        requiresRestart: true,
-        default: {},
-        description: 'Experimental tool features.',
-        showInDialog: false,
-        properties: {
-          skills: {
-            type: 'boolean',
-            label: 'Skills',
-            category: 'Tools',
-            requiresRestart: true,
-            default: false,
-            description:
-              'Enable experimental Agent Skills feature. When enabled, Qwen Code can use Skills from .qwen/skills/ and ~/.qwen/skills/.',
-            showInDialog: true,
-          },
-        },
-      },
     },
   },
 
@@ -1219,6 +1198,16 @@ const SETTINGS_SCHEMA = {
     description: 'Setting to enable experimental features',
     showInDialog: false,
     properties: {
+      skills: {
+        type: 'boolean',
+        label: 'Skills',
+        category: 'Experimental',
+        requiresRestart: true,
+        default: false,
+        description:
+          'Enable experimental Agent Skills feature. When enabled, Qwen Code can use Skills from .qwen/skills/ and ~/.qwen/skills/.',
+        showInDialog: true,
+      },
       extensionManagement: {
         type: 'boolean',
         label: 'Extension Management',