diff --git a/package.json b/package.json
index bf98e7676..1d0cd2a61 100644
--- a/package.json
+++ b/package.json
@@ -11,6 +11,7 @@
     "prepack": "lerna run --stream prepack",
     "dev": "lerna run --stream prepack -- --incremental && lerna --ignore=@logto/integration-test run --parallel dev",
     "start": "cd packages/core && NODE_ENV=production node . --from-root",
+    "migration-deploy": "cd packages/core && pnpm migration-deploy",
     "ci:build": "lerna run --stream build",
     "ci:lint": "lerna run --parallel lint",
     "ci:stylelint": "lerna run --parallel stylelint",
diff --git a/packages/core/src/env-set/check-migration-state.ts b/packages/core/src/env-set/check-migration-state.ts
new file mode 100644
index 000000000..6ce0c13cb
--- /dev/null
+++ b/packages/core/src/env-set/check-migration-state.ts
@@ -0,0 +1,34 @@
+import inquirer from 'inquirer';
+import { DatabasePool } from 'slonik';
+
+import { getUndeployedMigrations, runMigrations } from '@/migration';
+
+import { allYes } from './parameters';
+
+export const checkMigrationState = async (pool: DatabasePool) => {
+  const migrations = await getUndeployedMigrations(pool);
+
+  if (migrations.length === 0) {
+    return;
+  }
+
+  const error = new Error(
+    `Found undeployed migrations, you must deploy them first by "pnpm migration-deploy" command, reference: https://docs.logto.io/docs/recipes/deployment/#migration`
+  );
+
+  if (allYes) {
+    throw error;
+  }
+
+  const deploy = await inquirer.prompt({
+    type: 'confirm',
+    name: 'value',
+    message: `Found undeployed migrations, would you like to deploy now?`,
+  });
+
+  if (!deploy.value) {
+    throw error;
+  }
+
+  await runMigrations(pool);
+};
diff --git a/packages/core/src/env-set/index.ts b/packages/core/src/env-set/index.ts
index 2f7487375..3383417e5 100644
--- a/packages/core/src/env-set/index.ts
+++ b/packages/core/src/env-set/index.ts
@@ -6,6 +6,7 @@ import { DatabasePool } from 'slonik';
 import { appendPath } from '@/utils/url';
 
 import { addConnectors } from './add-connectors';
+import { checkMigrationState } from './check-migration-state';
 import createPoolByEnv from './create-pool-by-env';
 import loadOidcValues from './oidc';
 import { isTrue } from './parameters';
@@ -80,6 +81,10 @@ function createEnvSet() {
       values = await loadEnvValues();
       pool = await createPoolByEnv(values.isTest);
       await addConnectors(values.connectorDirectory);
+
+      if (pool) {
+        await checkMigrationState(pool);
+      }
     },
   };
 }
diff --git a/packages/core/src/migration/index.test.ts b/packages/core/src/migration/index.test.ts
index 7e773b1a6..f1d87a33d 100644
--- a/packages/core/src/migration/index.test.ts
+++ b/packages/core/src/migration/index.test.ts
@@ -22,17 +22,6 @@ const pool = createMockPool({
   },
 });
 const { table, fields } = convertToIdentifiers(LogtoConfigs);
-const existsSync = jest.fn();
-const readdir = jest.fn();
-
-jest.mock('fs', () => ({
-  existsSync: () => existsSync(),
-}));
-
-jest.mock('fs/promises', () => ({
-  ...jest.requireActual('fs/promises'),
-  readdir: async () => readdir(),
-}));
 
 describe('isLogtoConfigsTableExists()', () => {
   it('generates "select exists" sql and query for result', async () => {
@@ -171,20 +160,6 @@ describe('updateDatabaseVersion()', () => {
   });
 });
 
-describe('getMigrationFiles()', () => {
-  it('returns [] if directory does not exist', async () => {
-    existsSync.mockReturnValueOnce(false);
-    await expect(getMigrationFiles()).resolves.toEqual([]);
-  });
-
-  it('returns files without "next"', async () => {
-    existsSync.mockReturnValueOnce(true);
-    readdir.mockResolvedValueOnce(['next.js', '1.0.0.js', '1.0.2.js', '1.0.1.js']);
-
-    await expect(getMigrationFiles()).resolves.toEqual(['1.0.0.js', '1.0.2.js', '1.0.1.js']);
-  });
-});
-
 describe('getUndeployedMigrations()', () => {
   beforeEach(() => {
     jest