diff --git a/backend/src/database/db.js b/backend/src/database/db.js
index db46d4c..324712d 100644
--- a/backend/src/database/db.js
+++ b/backend/src/database/db.js
@@ -1,7 +1,28 @@
+const fs = require('fs');
+const path = require('path');
 const knex = require('knex');
 const knexConfig = require('../../knexfile');
 const logger = require('../utils/logger');
 
+// Ensure SQLite directory exists when using file-based DB (native installs)
+try {
+  const isPostgres = knexConfig && knexConfig.client === 'pg';
+  if (!isPostgres && knexConfig && knexConfig.connection) {
+    const filename = typeof knexConfig.connection === 'object'
+      ? knexConfig.connection.filename
+      : (typeof knexConfig.connection === 'string' ? knexConfig.connection : null);
+    if (filename && typeof filename === 'string') {
+      const dir = path.dirname(filename);
+      if (dir && dir !== '.') {
+        fs.mkdirSync(dir, { recursive: true });
+      }
+    }
+  }
+} catch (e) {
+  // Non-fatal: log and continue; SQLite will fail later if still missing
+  try { logger.warn('SQLite directory ensure failed', { error: e.message }); } catch (_) {}
+}
+
 // Create database connection with built-in retry logic
 const db = knex(knexConfig);
 
@@ -312,4 +333,4 @@ async function logActivity(activityType, metadata = {}, eventId = null, actor =
   }
 }
 
-module.exports = { db, initializeDatabase, logActivity, withRetry };
\ No newline at end of file
+module.exports = { db, initializeDatabase, logActivity, withRetry };
diff --git a/scripts/setup.sh b/scripts/setup.sh
index 8874b45..15a6de1 100755
--- a/scripts/setup.sh
+++ b/scripts/setup.sh
@@ -569,6 +569,9 @@ setup_native_installation() {
     cd "$NATIVE_APP_DIR/app/backend"
     npm install --production
     
+    # Ensure SQLite data directory exists for native installs
+    mkdir -p "$NATIVE_APP_DIR/app/backend/data"
+    
     # Generate secrets
     local jwt_secret=$(generate_jwt_secret)
     [[ -z "$ADMIN_PASSWORD" ]] && ADMIN_PASSWORD=$(generate_password)