diff --git a/packages/core/src/__mocks__/user.ts b/packages/core/src/__mocks__/user.ts
index 35ec77dbc..f9883193e 100644
--- a/packages/core/src/__mocks__/user.ts
+++ b/packages/core/src/__mocks__/user.ts
@@ -15,6 +15,7 @@ export const mockUser: User = {
   identities: {
     connector1: { userId: 'connector1', details: {} },
   },
+  logtoConfig: {},
   mfaVerifications: [],
   customData: {},
   applicationId: 'bar',
@@ -69,6 +70,7 @@ export const mockUserWithPassword: User = {
     connector1: { userId: 'connector1', details: {} },
   },
   customData: {},
+  logtoConfig: {},
   mfaVerifications: [],
   applicationId: 'bar',
   lastSignInAt: 1_650_969_465_789,
@@ -89,6 +91,7 @@ export const mockUserList: User[] = [
     avatar: null,
     identities: {},
     customData: {},
+    logtoConfig: {},
     mfaVerifications: [],
     applicationId: 'bar',
     lastSignInAt: 1_650_969_465_000,
@@ -107,6 +110,7 @@ export const mockUserList: User[] = [
     avatar: null,
     identities: {},
     customData: {},
+    logtoConfig: {},
     mfaVerifications: [],
     applicationId: 'bar',
     lastSignInAt: 1_650_969_465_000,
@@ -125,6 +129,7 @@ export const mockUserList: User[] = [
     avatar: null,
     identities: {},
     customData: {},
+    logtoConfig: {},
     mfaVerifications: [],
     applicationId: 'bar',
     lastSignInAt: 1_650_969_465_000,
@@ -143,6 +148,7 @@ export const mockUserList: User[] = [
     avatar: null,
     identities: {},
     customData: {},
+    logtoConfig: {},
     mfaVerifications: [],
     applicationId: 'bar',
     lastSignInAt: 1_650_969_465_000,
@@ -161,6 +167,7 @@ export const mockUserList: User[] = [
     avatar: null,
     identities: {},
     customData: {},
+    logtoConfig: {},
     mfaVerifications: [],
     applicationId: 'bar',
     lastSignInAt: 1_650_969_465_000,
diff --git a/packages/core/src/queries/user.test.ts b/packages/core/src/queries/user.test.ts
index 6cd7daeef..81beaad58 100644
--- a/packages/core/src/queries/user.test.ts
+++ b/packages/core/src/queries/user.test.ts
@@ -39,6 +39,7 @@ describe('user query', () => {
     ...mockUser,
     identities: JSON.stringify(mockUser.identities),
     customData: JSON.stringify(mockUser.customData),
+    logtoConfig: JSON.stringify(mockUser.logtoConfig),
     mfaVerifications: JSON.stringify(mockUser.mfaVerifications),
   };
 
@@ -272,6 +273,7 @@ describe('user query', () => {
       ...mockUser,
       identities: JSON.stringify(restIdentities),
       customData: JSON.stringify(mockUser.customData),
+      logtoConfig: JSON.stringify(mockUser.logtoConfig),
       mfaVerifications: JSON.stringify(mockUser.mfaVerifications),
     };
 
diff --git a/packages/core/src/routes/interaction/actions/submit-interaction.test.ts b/packages/core/src/routes/interaction/actions/submit-interaction.test.ts
index b704bb6ea..0dea2ab9a 100644
--- a/packages/core/src/routes/interaction/actions/submit-interaction.test.ts
+++ b/packages/core/src/routes/interaction/actions/submit-interaction.test.ts
@@ -183,7 +183,7 @@ describe('submit action', () => {
       {
         id: 'uid',
         ...upsertProfile,
-        customData: {
+        logtoConfig: {
           [userMfaDataKey]: {
             skipped: true,
           },
@@ -348,7 +348,7 @@ describe('submit action', () => {
         google: { userId: 'googleId', details: {} },
       },
       lastSignInAt: now,
-      customData: {
+      logtoConfig: {
         [userMfaDataKey]: {
           skipped: true,
         },
diff --git a/packages/core/src/routes/interaction/actions/submit-interaction.ts b/packages/core/src/routes/interaction/actions/submit-interaction.ts
index 3c72e46f6..6627293af 100644
--- a/packages/core/src/routes/interaction/actions/submit-interaction.ts
+++ b/packages/core/src/routes/interaction/actions/submit-interaction.ts
@@ -118,7 +118,7 @@ async function handleSubmitRegister(
       ),
       ...conditional(
         mfaSkipped && {
-          customData: {
+          logtoConfig: {
             [userMfaDataKey]: {
               skipped: true,
             },
@@ -174,8 +174,8 @@ async function handleSubmitSignIn(
     ),
     ...conditional(
       mfaSkipped && {
-        customData: {
-          ...user.customData,
+        logtoConfig: {
+          ...user.logtoConfig,
           [userMfaDataKey]: {
             skipped: true,
           },
diff --git a/packages/core/src/routes/interaction/verifications/mfa-verification.test.ts b/packages/core/src/routes/interaction/verifications/mfa-verification.test.ts
index b54f2c9ea..e561293aa 100644
--- a/packages/core/src/routes/interaction/verifications/mfa-verification.test.ts
+++ b/packages/core/src/routes/interaction/verifications/mfa-verification.test.ts
@@ -200,7 +200,7 @@ describe('validateMandatoryBindMfa', () => {
     it('user mfaVerifications and bindMfa missing, mark skipped, and not required should pass', async () => {
       findUserById.mockResolvedValueOnce({
         ...mockUser,
-        customData: {
+        logtoConfig: {
           mfa: { skipped: true },
         },
       });
diff --git a/packages/core/src/routes/interaction/verifications/mfa-verification.ts b/packages/core/src/routes/interaction/verifications/mfa-verification.ts
index 67c4de7fb..8d08e5437 100644
--- a/packages/core/src/routes/interaction/verifications/mfa-verification.ts
+++ b/packages/core/src/routes/interaction/verifications/mfa-verification.ts
@@ -126,15 +126,29 @@ export const userMfaDataKey = 'mfa';
 /**
  * Check if the user has skipped MFA binding
  */
-const isMfaSkipped = (customData: JsonObject): boolean => {
+const isMfaSkipped = (logtoConfig: JsonObject): boolean => {
   const userMfaDataGuard = z.object({
     skipped: z.boolean().optional(),
   });
 
-  const parsed = z.object({ [userMfaDataKey]: userMfaDataGuard }).safeParse(customData);
+  const parsed = z.object({ [userMfaDataKey]: userMfaDataGuard }).safeParse(logtoConfig);
 
   return parsed.success ? parsed.data[userMfaDataKey].skipped === true : false;
 };
+/**
+ * Mark MFA as skipped in user custom data
+ */
+export const markMfaSkipped = async (tenant: TenantContext, accountId: string) => {
+  const { customData } = await tenant.queries.users.findUserById(accountId);
+  await tenant.queries.users.updateUserById(accountId, {
+    customData: {
+      ...customData,
+      [userMfaDataKey]: {
+        skipped: true,
+      },
+    },
+  });
+};
 
 export const validateMandatoryBindMfa = async (
   tenant: TenantContext,
@@ -168,9 +182,9 @@ export const validateMandatoryBindMfa = async (
 
   if (event === InteractionEvent.SignIn) {
     const { accountId } = interaction;
-    const { mfaVerifications, customData } = await tenant.queries.users.findUserById(accountId);
+    const { mfaVerifications, logtoConfig } = await tenant.queries.users.findUserById(accountId);
 
-    if (isMfaSkipped(customData)) {
+    if (isMfaSkipped(logtoConfig)) {
       return interaction;
     }
 
diff --git a/packages/schemas/alterations/next-1698910485-user-logto-data.ts b/packages/schemas/alterations/next-1698910485-user-logto-data.ts
new file mode 100644
index 000000000..29d5a98df
--- /dev/null
+++ b/packages/schemas/alterations/next-1698910485-user-logto-data.ts
@@ -0,0 +1,20 @@
+import { sql } from 'slonik';
+
+import type { AlterationScript } from '../lib/types/alteration.js';
+
+const alteration: AlterationScript = {
+  up: async (pool) => {
+    await pool.query(sql`
+      alter table users
+        add column if not exists logto_config jsonb not null default '{}'::jsonb;
+    `);
+  },
+  down: async (pool) => {
+    await pool.query(sql`
+      alter table users
+        drop column logto_config;
+    `);
+  },
+};
+
+export default alteration;
diff --git a/packages/schemas/tables/users.sql b/packages/schemas/tables/users.sql
index b72c95325..e873e6b71 100644
--- a/packages/schemas/tables/users.sql
+++ b/packages/schemas/tables/users.sql
@@ -16,6 +16,7 @@ create table users (
   application_id varchar(21),
   identities jsonb /* @use Identities */ not null default '{}'::jsonb,
   custom_data jsonb /* @use JsonObject */ not null default '{}'::jsonb,
+  logto_config jsonb /* @use JsonObject */ not null default '{}'::jsonb,
   mfa_verifications jsonb /* @use MfaVerifications */ not null default '[]'::jsonb,
   is_suspended boolean not null default false,
   last_sign_in_at timestamptz,