diff --git a/packages/cli/src/commands/$default.ts b/packages/cli/src/commands/$default.ts
index 48cb3ef..b50ac44 100644
--- a/packages/cli/src/commands/$default.ts
+++ b/packages/cli/src/commands/$default.ts
@@ -107,12 +107,25 @@ export const command: CommandModule<SharedOptions, DefaultArgs> = {
 
       if (providerSettings) {
         const { keyName } = providerSettings;
-        const apiKey = process.env[keyName];
+        
+        // First check if the API key is in the config
+        const configApiKey = userConfig[keyName as keyof typeof userConfig] as string;
+        // Then fall back to environment variable
+        const envApiKey = process.env[keyName];
+        // Use config key if available, otherwise use env key
+        const apiKey = configApiKey || envApiKey;
 
         if (!apiKey) {
           logger.error(getProviderApiKeyError(userModelProvider));
           throw new Error(`${userModelProvider} API key not found`);
         }
+        
+        // If we're using a key from config, set it as an environment variable
+        // This ensures it's available to the provider libraries
+        if (configApiKey && !envApiKey) {
+          process.env[keyName] = configApiKey;
+          logger.debug(`Using ${keyName} from configuration`);
+        }
       }
       // No API key check needed for Ollama as it uses a local server
 
diff --git a/packages/cli/src/commands/config.ts b/packages/cli/src/commands/config.ts
index 8ff72d5..caed533 100644
--- a/packages/cli/src/commands/config.ts
+++ b/packages/cli/src/commands/config.ts
@@ -73,6 +73,10 @@ export const command: CommandModule<SharedOptions, ConfigOptions> = {
         '$0 config clear customPrompt',
         'Reset customPrompt to default value',
       )
+      .example(
+        '$0 config set ANTHROPIC_API_KEY <your-key>',
+        'Store your Anthropic API key in configuration',
+      )
       .example(
         '$0 config clear --all',
         'Clear all configuration settings',
@@ -151,6 +155,30 @@ export const command: CommandModule<SharedOptions, ConfigOptions> = {
         return;
       }
 
+      // Check if this is an API key and add a warning
+      if (argv.key.includes('API_KEY')) {
+        logger.warn(
+          chalk.yellow(
+            'Warning: Storing API keys in configuration is less secure than using environment variables.'
+          )
+        );
+        logger.warn(
+          chalk.yellow(
+            'Your API key will be stored in plaintext in the configuration file.'
+          )
+        );
+        
+        // Ask for confirmation
+        const isConfirmed = await confirm(
+          'Do you want to continue storing your API key in the configuration?'
+        );
+        
+        if (!isConfirmed) {
+          logger.info('Operation cancelled.');
+          return;
+        }
+      }
+
       // Parse the value based on current type or infer boolean/number
       let parsedValue: string | boolean | number = argv.value;
 
diff --git a/packages/cli/src/settings/config.ts b/packages/cli/src/settings/config.ts
index 4501378..7c3c730 100644
--- a/packages/cli/src/settings/config.ts
+++ b/packages/cli/src/settings/config.ts
@@ -20,6 +20,11 @@ const defaultConfig = {
   customPrompt: '',
   profile: false,
   tokenCache: true,
+  // API keys (empty by default)
+  ANTHROPIC_API_KEY: '',
+  OPENAI_API_KEY: '',
+  XAI_API_KEY: '',
+  MISTRAL_API_KEY: '',
 };
 
 export type Config = typeof defaultConfig;
diff --git a/packages/cli/tests/settings/config.test.ts b/packages/cli/tests/settings/config.test.ts
index 814c82a..75b0c1b 100644
--- a/packages/cli/tests/settings/config.test.ts
+++ b/packages/cli/tests/settings/config.test.ts
@@ -49,6 +49,11 @@ describe('Config', () => {
         profile: false,
         customPrompt: '',
         tokenCache: true,
+        // API keys
+        ANTHROPIC_API_KEY: '',
+        OPENAI_API_KEY: '',
+        XAI_API_KEY: '',
+        MISTRAL_API_KEY: '',
       });
       expect(fs.existsSync).toHaveBeenCalledWith(mockConfigFile);
     });
@@ -86,6 +91,11 @@ describe('Config', () => {
         profile: false,
         customPrompt: '',
         tokenCache: true,
+        // API keys
+        ANTHROPIC_API_KEY: '',
+        OPENAI_API_KEY: '',
+        XAI_API_KEY: '',
+        MISTRAL_API_KEY: '',
       });
     });
   });
@@ -117,4 +127,4 @@ describe('Config', () => {
       expect(result).toEqual({ githubMode: true, existingSetting: 'value' });
     });
   });
-});
+});
\ No newline at end of file