diff --git a/src/config/io.ts b/src/config/io.ts
index 1b6fe79..045000e 100644
--- a/src/config/io.ts
+++ b/src/config/io.ts
@@ -143,14 +143,13 @@ export function configToEnv(config: LettaBotConfig): Record<string, string> {
 }
 
 /**
- * Apply config to process.env
+ * Apply config to process.env (YAML config takes priority over .env)
  */
 export function applyConfigToEnv(config: LettaBotConfig): void {
   const env = configToEnv(config);
   for (const [key, value] of Object.entries(env)) {
-    if (!process.env[key]) {
-      process.env[key] = value;
-    }
+    // YAML config always takes priority
+    process.env[key] = value;
   }
 }
 
diff --git a/src/main.ts b/src/main.ts
index 9c92d55..cf61151 100644
--- a/src/main.ts
+++ b/src/main.ts
@@ -5,13 +5,15 @@
  * Chat continues seamlessly between Telegram, Slack, and WhatsApp.
  */
 
+// Load .env first for backwards compatibility
 import 'dotenv/config';
+
 import { createServer } from 'node:http';
 import { existsSync, mkdirSync, readFileSync, readdirSync } from 'node:fs';
 import { resolve } from 'node:path';
 import { spawn } from 'node:child_process';
 
-// Load YAML config and apply to process.env (before other imports)
+// Load YAML config and apply to process.env (overrides .env values)
 import { loadConfig, applyConfigToEnv, syncProviders, resolveConfigPath } from './config/index.js';
 const yamlConfig = loadConfig();
 console.log(`[Config] Loaded from ${resolveConfigPath()}`);