diff --git a/package-lock.json b/package-lock.json
index 66ed265..656441b 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -16,7 +16,8 @@
                 "debug": "^4.4.3",
                 "dotenv": "^17.4.2",
                 "hono": "^4.12.26",
-                "kysely": "^0.29.2",
+                "kysely": "^0.29.4",
+                "kysely-node-native-sqlite": "^1.0.1",
                 "ws": "^8.21.0",
                 "zod": "^4.4.3"
             },
@@ -8314,6 +8315,15 @@
                 "node": ">=22.0.0"
             }
         },
+        "node_modules/kysely-node-native-sqlite": {
+            "version": "1.0.1",
+            "resolved": "https://registry.npmjs.org/kysely-node-native-sqlite/-/kysely-node-native-sqlite-1.0.1.tgz",
+            "integrity": "sha512-FHty4bi885waQMMMw2P9F+mqZUdozd1OBWQI72CffsQzbZhcOgsz3jpZRTUM1xAtG1wkz/VQAj3JavQvCdhL2w==",
+            "license": "ISC",
+            "peerDependencies": {
+                "kysely": ">=0.27.0"
+            }
+        },
         "node_modules/language-subtag-registry": {
             "version": "0.3.23",
             "resolved": "https://registry.npmjs.org/language-subtag-registry/-/language-subtag-registry-0.3.23.tgz",
diff --git a/package.json b/package.json
index eca8a9a..0a5bf01 100644
--- a/package.json
+++ b/package.json
@@ -51,7 +51,8 @@
         "debug": "^4.4.3",
         "dotenv": "^17.4.2",
         "hono": "^4.12.26",
-        "kysely": "^0.29.2",
+        "kysely": "^0.29.4",
+        "kysely-node-native-sqlite": "^1.0.1",
         "ws": "^8.21.0",
         "zod": "^4.4.3"
     },
diff --git a/src/app.ts b/src/app.ts
new file mode 100644
index 0000000..08df05e
--- /dev/null
+++ b/src/app.ts
@@ -0,0 +1,59 @@
+import { Config } from './services/config.ts';
+import { Database, MigrationService } from './services/storage/index.ts';
+import { Logger } from './utils/logger.ts';
+
+/** Application composition root. */
+export class App {
+    /**
+     * Construct infrastructure and validate all routes before returning a runnable app.
+     */
+    static async create(): Promise<App> {
+        const config = Config.fromEnv();
+        const debug = new Logger('sync-server-v2');
+        debug('config loaded: %O', config);
+
+        // Persistence must be ready before routes accept traffic.
+        const database = new Database({ path: config.database.path, debug });
+        const migrations = new MigrationService(database, debug);
+        await migrations.migrateToLatest();
+
+        return new App(database);
+    }
+
+    private stopPromise: Promise<void> | undefined;
+
+    constructor(private readonly database: Database) {}
+
+    async start(): Promise<void> {}
+
+    /** Stop transports before releasing the database they may still use. */
+    async stop(): Promise<void> {
+        this.stopPromise ??= this.database.destroy();
+        await this.stopPromise;
+    }
+}
+
+const app = await App.create();
+let shuttingDown = false;
+
+const shutdown = (signal: NodeJS.Signals): void => {
+    if (shuttingDown) {
+        return;
+    }
+
+    shuttingDown = true;
+    void app.stop().catch((error) => {
+        console.error('Graceful shutdown failed after ' + signal, error);
+        process.exitCode = 1;
+    });
+};
+
+process.once('SIGINT', (): void => shutdown('SIGINT'));
+process.once('SIGTERM', (): void => shutdown('SIGTERM'));
+
+try {
+    await app.start();
+} catch (error: unknown) {
+    await app.stop();
+    throw error;
+}
diff --git a/src/services/storage/database.ts b/src/services/storage/database.ts
index f89832b..c3ef093 100644
--- a/src/services/storage/database.ts
+++ b/src/services/storage/database.ts
@@ -1,5 +1,6 @@
-import DatabaseConstructor from 'better-sqlite3';
-import { Kysely, SqliteDialect } from 'kysely';
+import { CompiledQuery, Kysely } from 'kysely';
+import { NodeNativeSqliteDialect } from 'kysely-node-native-sqlite';
+
 import type { DatabaseTables } from './tables.ts';
 import type { Logger } from '../../utils/logger.ts';
 
@@ -13,13 +14,13 @@ export type DatabaseOptions = {
 };
 
 /**
- * Thin wrapper around better-sqlite3 and Kysely.
+ * Thin wrapper around Kysely and NodeNativeSqliteDialect (which uses node:sqlite).
  *
  * Owns connection setup, pragma configuration, and graceful teardown.
  */
 export class Database {
     private readonly debug: Logger;
-    private readonly sqlite: DatabaseConstructor.Database;
+    private readonly dialect: NodeNativeSqliteDialect;
     private readonly kysely: Kysely<DatabaseTables>;
 
     /**
@@ -32,13 +33,15 @@ export class Database {
         this.debug = options.debug.extend('database');
 
         // Create the SQLite database.
-        this.sqlite = new DatabaseConstructor(options.path);
-        this.configurePragmas();
+        this.dialect = new NodeNativeSqliteDialect(options.path);
 
         // Create the Kysely database.
         this.kysely = new Kysely<DatabaseTables>({
-            dialect: new SqliteDialect({ database: this.sqlite }),
+            dialect: this.dialect,
         });
+
+        // Configure the SQLite pragmas.
+        this.configurePragmas();
     }
 
     /**
@@ -65,7 +68,8 @@ export class Database {
      */
     private configurePragmas(): void {
         this.debug('configuring SQLite pragmas');
-        this.sqlite.pragma('journal_mode = WAL');
-        this.sqlite.pragma('foreign_keys = ON');
+
+        this.kysely.executeQuery(CompiledQuery.raw('PRAGMA journal_mode = WAL'));
+        this.kysely.executeQuery(CompiledQuery.raw('PRAGMA foreign_keys = ON'));
     }
 }
diff --git a/tsconfig.json b/tsconfig.json
index 2f84530..779ded5 100644
--- a/tsconfig.json
+++ b/tsconfig.json
@@ -12,7 +12,8 @@
         "allowImportingTsExtensions": true,
         "noEmit": true,
         "declaration": true,
-        "declarationMap": true
+        "declarationMap": true,
+        "types": ["node"]
     },
     "exclude": ["node_modules/**/*", "dist/**/*", "test"]
 }