diff --git a/src/backend/starter.ts b/src/backend/starter.ts
index f8b4c6ae..5da0ed37 100644
--- a/src/backend/starter.ts
+++ b/src/backend/starter.ts
@@ -19,9 +19,20 @@ import { systemLogger, versionLogger } from "./utils/logger.js";
     const envPath = path.join(dataDir, ".env");
     try {
       await fs.access(envPath);
-      dotenv.config({ path: envPath });
+      // Load the persistent .env file and override process.env
+      const persistentConfig = dotenv.config({ path: envPath });
+      if (persistentConfig.parsed) {
+        // Override process.env with values from persistent config
+        Object.assign(process.env, persistentConfig.parsed);
+      }
       systemLogger.info(`Loaded persistent configuration from ${envPath}`, {
-        operation: "config_load"
+        operation: "config_load",
+        hasDatabaseKey: !!persistentConfig.parsed?.DATABASE_KEY,
+        databaseKeyLength: persistentConfig.parsed?.DATABASE_KEY?.length || 0,
+        hasJwtSecret: !!persistentConfig.parsed?.JWT_SECRET,
+        jwtSecretLength: persistentConfig.parsed?.JWT_SECRET?.length || 0,
+        hasInternalAuthToken: !!persistentConfig.parsed?.INTERNAL_AUTH_TOKEN,
+        internalAuthTokenLength: persistentConfig.parsed?.INTERNAL_AUTH_TOKEN?.length || 0
       });
     } catch {
       // Config file doesn't exist yet, will be created on first run
diff --git a/src/backend/utils/system-crypto.ts b/src/backend/utils/system-crypto.ts
index 9283a553..5895dc6f 100644
--- a/src/backend/utils/system-crypto.ts
+++ b/src/backend/utils/system-crypto.ts
@@ -76,8 +76,19 @@ class SystemCrypto {
 
       // Check environment variable
       const envKey = process.env.DATABASE_KEY;
+      databaseLogger.info("Checking DATABASE_KEY from environment", {
+        operation: "db_key_check",
+        hasKey: !!envKey,
+        keyLength: envKey?.length || 0,
+        meetsLengthRequirement: envKey && envKey.length >= 64
+      });
+      
       if (envKey && envKey.length >= 64) {
         this.databaseKey = Buffer.from(envKey, 'hex');
+        databaseLogger.info("Using existing DATABASE_KEY from environment", {
+          operation: "db_key_use_existing",
+          keyLength: envKey.length
+        });
         return;
       }