diff --git a/packages/core/src/database/types.ts b/packages/core/src/database/types.ts
index 2a5d86b13..beae5eaf1 100644
--- a/packages/core/src/database/types.ts
+++ b/packages/core/src/database/types.ts
@@ -20,4 +20,5 @@ export type FindManyData<Schema extends SchemaLike> = {
 export type UpdateWhereData<Schema extends SchemaLike> = {
   set: Partial<Schema>;
   where: Partial<Schema>;
+  jsonbMode: 'replace' | 'merge';
 };
diff --git a/packages/core/src/database/update-where.test.ts b/packages/core/src/database/update-where.test.ts
index edfc3e87c..f99778e42 100644
--- a/packages/core/src/database/update-where.test.ts
+++ b/packages/core/src/database/update-where.test.ts
@@ -1,9 +1,10 @@
-import { CreateUser, Users, Applications } from '@logto/schemas';
+import { CreateUser, Users, Applications, User } from '@logto/schemas';
 
 import envSet from '@/env-set';
 import { UpdateError } from '@/errors/SlonikError';
 import { createTestPool } from '@/utils/test-utils';
 
+import { UpdateWhereData } from './types';
 import { buildUpdateWhere } from './update-where';
 
 const poolSpy = jest.spyOn(envSet, 'pool', 'get');
@@ -20,6 +21,7 @@ describe('buildUpdateWhere()', () => {
       updateWhere({
         set: { username: '123' },
         where: { id: 'foo', username: '456' },
+        jsonbMode: 'merge',
       })
     ).resolves.toBe(undefined);
   });
@@ -47,6 +49,7 @@ describe('buildUpdateWhere()', () => {
       updateWhere({
         set: { username: '123', primaryEmail: 'foo@bar.com', applicationId: 'bar' },
         where: { id: 'foo' },
+        jsonbMode: 'merge',
       })
     ).resolves.toStrictEqual(user);
   });
@@ -66,6 +69,7 @@ describe('buildUpdateWhere()', () => {
       updateWhere({
         set: { customClientMetadata: { idTokenTtl: 3600 } },
         where: { id: 'foo' },
+        jsonbMode: 'merge',
       })
     ).resolves.toStrictEqual({ id: 'foo', customClientMetadata: '{"idTokenTtl":3600}' });
   });
@@ -82,6 +86,7 @@ describe('buildUpdateWhere()', () => {
       updateWhere({
         set: { username: '123', id: undefined },
         where: { id: 'foo', username: '456' },
+        jsonbMode: 'merge',
       })
     ).rejects.toMatchError(new Error(`Cannot convert id to primitive`));
   });
@@ -91,7 +96,11 @@ describe('buildUpdateWhere()', () => {
     poolSpy.mockReturnValue(pool);
 
     const updateWhere = buildUpdateWhere(Users, true);
-    const updateWhereData = { set: { username: '123' }, where: { id: 'foo' } };
+    const updateWhereData: UpdateWhereData<User> = {
+      set: { username: '123' },
+      where: { id: 'foo' },
+      jsonbMode: 'merge',
+    };
 
     await expect(updateWhere(updateWhereData)).rejects.toMatchError(
       new UpdateError(Users, updateWhereData)
@@ -105,8 +114,14 @@ describe('buildUpdateWhere()', () => {
     poolSpy.mockReturnValue(pool);
 
     const updateWhere = buildUpdateWhere(Users, true);
-    const updateData = { set: { username: '123' }, where: { username: 'foo' } };
+    const updateWhereData: UpdateWhereData<User> = {
+      set: { username: '123' },
+      where: { username: 'foo' },
+      jsonbMode: 'merge',
+    };
 
-    await expect(updateWhere(updateData)).rejects.toMatchError(new UpdateError(Users, updateData));
+    await expect(updateWhere(updateWhereData)).rejects.toMatchError(
+      new UpdateError(Users, updateWhereData)
+    );
   });
 });
diff --git a/packages/core/src/database/update-where.ts b/packages/core/src/database/update-where.ts
index aff68d071..818bf1f90 100644
--- a/packages/core/src/database/update-where.ts
+++ b/packages/core/src/database/update-where.ts
@@ -29,14 +29,14 @@ export const buildUpdateWhere: BuildUpdateWhere = <
 ) => {
   const { table, fields } = convertToIdentifiers(schema);
   const isKeyOfSchema = isKeyOf(schema);
-  const connectKeyValueWithEqualSign = (data: Partial<Schema>) =>
+  const connectKeyValueWithEqualSign = (data: Partial<Schema>, jsonbMode: 'replace' | 'merge') =>
     Object.entries(data)
       .map(([key, value]) => {
         if (!isKeyOfSchema(key)) {
           return;
         }
 
-        if (value && typeof value === 'object' && !Array.isArray(value)) {
+        if (jsonbMode === 'merge' && value && typeof value === 'object' && !Array.isArray(value)) {
           /**
            * Jsonb || operator is used to shallow merge two jsonb types of data
            * all jsonb data field must be non-nullable
@@ -52,17 +52,17 @@ export const buildUpdateWhere: BuildUpdateWhere = <
       })
       .filter((value): value is Truthy<typeof value> => notFalsy(value));
 
-  return async ({ set, where }: UpdateWhereData<Schema>) => {
+  return async ({ set, where, jsonbMode }: UpdateWhereData<Schema>) => {
     const {
       rows: [data],
     } = await envSet.pool.query<ReturnType>(sql`
       update ${table}
-      set ${sql.join(connectKeyValueWithEqualSign(set), sql`, `)}
-      where ${sql.join(connectKeyValueWithEqualSign(where), sql` and `)}
+      set ${sql.join(connectKeyValueWithEqualSign(set, jsonbMode), sql`, `)}
+      where ${sql.join(connectKeyValueWithEqualSign(where, jsonbMode), sql` and `)}
       ${conditionalSql(returning, () => sql`returning *`)}
     `);
 
-    assertThat(!returning || data, new UpdateError(schema, { set, where }));
+    assertThat(!returning || data, new UpdateError(schema, { set, where, jsonbMode }));
 
     return data;
   };
diff --git a/packages/core/src/lib/passcode.ts b/packages/core/src/lib/passcode.ts
index 5cca0eb03..aab9ee712 100644
--- a/packages/core/src/lib/passcode.ts
+++ b/packages/core/src/lib/passcode.ts
@@ -107,9 +107,13 @@ export const verifyPasscode = async (
 
   if (code !== passcode.code) {
     // TODO use SQL's native +1
-    await updatePasscode({ where: { id: passcode.id }, set: { tryCount: passcode.tryCount + 1 } });
+    await updatePasscode({
+      where: { id: passcode.id },
+      set: { tryCount: passcode.tryCount + 1 },
+      jsonbMode: 'merge',
+    });
     throw new RequestError('passcode.code_mismatch');
   }
 
-  await updatePasscode({ where: { id: passcode.id }, set: { consumed: true } });
+  await updatePasscode({ where: { id: passcode.id }, set: { consumed: true }, jsonbMode: 'merge' });
 };
diff --git a/packages/core/src/middleware/koa-slonik-error-handler.test.ts b/packages/core/src/middleware/koa-slonik-error-handler.test.ts
index e276f9081..321a13efc 100644
--- a/packages/core/src/middleware/koa-slonik-error-handler.test.ts
+++ b/packages/core/src/middleware/koa-slonik-error-handler.test.ts
@@ -50,7 +50,11 @@ describe('koaSlonikErrorHandler middleware', () => {
   });
 
   it('Update Error', async () => {
-    const error = new UpdateError(Users, { set: { name: 'punk' }, where: { id: '123' } });
+    const error = new UpdateError(Users, {
+      set: { name: 'punk' },
+      where: { id: '123' },
+      jsonbMode: 'merge',
+    });
     next.mockImplementationOnce(() => {
       throw error;
     });
diff --git a/packages/core/src/queries/application.ts b/packages/core/src/queries/application.ts
index c26b65fc3..c29254790 100644
--- a/packages/core/src/queries/application.ts
+++ b/packages/core/src/queries/application.ts
@@ -43,8 +43,9 @@ const updateApplication = buildUpdateWhere<CreateApplication, Application>(Appli
 
 export const updateApplicationById = async (
   id: string,
-  set: Partial<OmitAutoSetFields<CreateApplication>>
-) => updateApplication({ set, where: { id } });
+  set: Partial<OmitAutoSetFields<CreateApplication>>,
+  jsonbMode: 'replace' | 'merge' = 'merge'
+) => updateApplication({ set, where: { id }, jsonbMode });
 
 export const deleteApplicationById = async (id: string) => {
   const { rowCount } = await envSet.pool.query(sql`
diff --git a/packages/core/src/queries/connector.test.ts b/packages/core/src/queries/connector.test.ts
index 25fa4689c..4fe20f2ac 100644
--- a/packages/core/src/queries/connector.test.ts
+++ b/packages/core/src/queries/connector.test.ts
@@ -80,7 +80,9 @@ describe('connector queries', () => {
       return createMockQueryResult([{ id, enabled }]);
     });
 
-    await expect(updateConnector({ where: { id }, set: { enabled } })).resolves.toEqual({
+    await expect(
+      updateConnector({ where: { id }, set: { enabled }, jsonbMode: 'merge' })
+    ).resolves.toEqual({
       id,
       enabled,
     });
diff --git a/packages/core/src/queries/passcode.test.ts b/packages/core/src/queries/passcode.test.ts
index 9a232f74d..f598110f8 100644
--- a/packages/core/src/queries/passcode.test.ts
+++ b/packages/core/src/queries/passcode.test.ts
@@ -112,7 +112,9 @@ describe('passcode query', () => {
       return createMockQueryResult([{ ...mockPasscode, tryCount }]);
     });
 
-    await expect(updatePasscode({ where: { id }, set: { tryCount } })).resolves.toEqual({
+    await expect(
+      updatePasscode({ where: { id }, set: { tryCount }, jsonbMode: 'merge' })
+    ).resolves.toEqual({
       ...mockPasscode,
       tryCount,
     });
diff --git a/packages/core/src/queries/resource.ts b/packages/core/src/queries/resource.ts
index f9d028078..4eb0195d8 100644
--- a/packages/core/src/queries/resource.ts
+++ b/packages/core/src/queries/resource.ts
@@ -49,8 +49,9 @@ const updateResource = buildUpdateWhere<CreateResource, Resource>(Resources, tru
 
 export const updateResourceById = async (
   id: string,
-  set: Partial<OmitAutoSetFields<CreateResource>>
-) => updateResource({ set, where: { id } });
+  set: Partial<OmitAutoSetFields<CreateResource>>,
+  jsonbMode: 'replace' | 'merge' = 'merge'
+) => updateResource({ set, where: { id }, jsonbMode });
 
 export const deleteResourceById = async (id: string) => {
   const { rowCount } = await envSet.pool.query(sql`
diff --git a/packages/core/src/queries/setting.ts b/packages/core/src/queries/setting.ts
index e410e8323..a8b902d0b 100644
--- a/packages/core/src/queries/setting.ts
+++ b/packages/core/src/queries/setting.ts
@@ -16,9 +16,12 @@ export const getSetting = async () =>
     where ${fields.id}=${defaultSettingId}
   `);
 
-export const updateSetting = async (setting: Partial<OmitAutoSetFields<CreateSetting>>) => {
+export const updateSetting = async (
+  setting: Partial<OmitAutoSetFields<CreateSetting>>,
+  jsonbMode: 'replace' | 'merge' = 'merge'
+) => {
   return buildUpdateWhere<CreateSetting, Setting>(
     Settings,
     true
-  )({ set: setting, where: { id: defaultSettingId } });
+  )({ set: setting, where: { id: defaultSettingId }, jsonbMode });
 };
diff --git a/packages/core/src/queries/sign-in-experience.ts b/packages/core/src/queries/sign-in-experience.ts
index 41f16147d..40a58a390 100644
--- a/packages/core/src/queries/sign-in-experience.ts
+++ b/packages/core/src/queries/sign-in-experience.ts
@@ -14,8 +14,10 @@ const updateSignInExperience = buildUpdateWhere<CreateSignInExperience, SignInEx
 
 const id = 'default';
 
-export const updateDefaultSignInExperience = async (set: Partial<CreateSignInExperience>) =>
-  updateSignInExperience({ set, where: { id } });
+export const updateDefaultSignInExperience = async (
+  set: Partial<CreateSignInExperience>,
+  jsonbMode: 'replace' | 'merge' = 'merge'
+) => updateSignInExperience({ set, where: { id }, jsonbMode });
 
 export const findDefaultSignInExperience = async () =>
   envSet.pool.one<SignInExperience>(sql`
diff --git a/packages/core/src/queries/user.ts b/packages/core/src/queries/user.ts
index 1079d2d01..5ee09e8c6 100644
--- a/packages/core/src/queries/user.ts
+++ b/packages/core/src/queries/user.ts
@@ -114,8 +114,11 @@ export const findUsers = async (limit: number, offset: number, search?: string)
 
 const updateUser = buildUpdateWhere<CreateUser, User>(Users, true);
 
-export const updateUserById = async (id: string, set: Partial<OmitAutoSetFields<CreateUser>>) =>
-  updateUser({ set, where: { id } });
+export const updateUserById = async (
+  id: string,
+  set: Partial<OmitAutoSetFields<CreateUser>>,
+  jsonbMode: 'replace' | 'merge' = 'merge'
+) => updateUser({ set, where: { id }, jsonbMode });
 
 export const deleteUserById = async (id: string) => {
   const { rowCount } = await envSet.pool.query(sql`
@@ -136,7 +139,7 @@ export const clearUserCustomDataById = async (id: string) => {
   `);
 
   if (rowCount < 1) {
-    throw new UpdateError(Users, { set: { customData: {} }, where: { id } });
+    throw new UpdateError(Users, { set: { customData: {} }, where: { id }, jsonbMode: 'replace' });
   }
 };
 
diff --git a/packages/core/src/routes/connector.ts b/packages/core/src/routes/connector.ts
index de89ef420..ebaf15ac7 100644
--- a/packages/core/src/routes/connector.ts
+++ b/packages/core/src/routes/connector.ts
@@ -108,12 +108,16 @@ export default function connectorRoutes<T extends AuthedRouter>(router: T) {
                 connector.metadata.type === metadata.type && connector.connector.enabled
             )
             .map(async ({ connector: { id } }) =>
-              updateConnector({ set: { enabled: false }, where: { id } })
+              updateConnector({ set: { enabled: false }, where: { id }, jsonbMode: 'merge' })
             )
         );
       }
 
-      const connector = await updateConnector({ set: { enabled }, where: { id } });
+      const connector = await updateConnector({
+        set: { enabled },
+        where: { id },
+        jsonbMode: 'merge',
+      });
       ctx.body = { ...connector, metadata };
 
       return next();
@@ -137,7 +141,7 @@ export default function connectorRoutes<T extends AuthedRouter>(router: T) {
         await validateConfig(body.config);
       }
 
-      const connector = await updateConnector({ set: body, where: { id } });
+      const connector = await updateConnector({ set: body, where: { id }, jsonbMode: 'replace' });
       ctx.body = { ...connector, metadata };
 
       return next();
diff --git a/packages/core/src/routes/connector.update.test.ts b/packages/core/src/routes/connector.update.test.ts
index 3e172f9fe..d20e62832 100644
--- a/packages/core/src/routes/connector.update.test.ts
+++ b/packages/core/src/routes/connector.update.test.ts
@@ -88,6 +88,7 @@ describe('connector PATCH routes', () => {
         expect.objectContaining({
           where: { id: 'id' },
           set: { enabled: true },
+          jsonbMode: 'merge',
         })
       );
       expect(response.body).toMatchObject({
@@ -126,6 +127,7 @@ describe('connector PATCH routes', () => {
         expect.objectContaining({
           where: { id: 'id' },
           set: { enabled: false },
+          jsonbMode: 'merge',
         })
       );
       expect(response.body).toMatchObject({
@@ -160,6 +162,7 @@ describe('connector PATCH routes', () => {
         expect.objectContaining({
           where: { id: 'id1' },
           set: { enabled: false },
+          jsonbMode: 'merge',
         })
       );
       expect(updateConnector).toHaveBeenNthCalledWith(
@@ -167,6 +170,7 @@ describe('connector PATCH routes', () => {
         expect.objectContaining({
           where: { id: 'id5' },
           set: { enabled: false },
+          jsonbMode: 'merge',
         })
       );
       expect(updateConnector).toHaveBeenNthCalledWith(
@@ -174,6 +178,7 @@ describe('connector PATCH routes', () => {
         expect.objectContaining({
           where: { id: 'id1' },
           set: { enabled: true },
+          jsonbMode: 'merge',
         })
       );
       expect(response.body).toMatchObject({
@@ -214,6 +219,7 @@ describe('connector PATCH routes', () => {
         expect.objectContaining({
           where: { id: 'id' },
           set: { enabled: false },
+          jsonbMode: 'merge',
         })
       );
       expect(response.body).toMatchObject({
@@ -270,6 +276,7 @@ describe('connector PATCH routes', () => {
         expect.objectContaining({
           where: { id: 'id' },
           set: { config: { cliend_id: 'client_id', client_secret: 'client_secret' } },
+          jsonbMode: 'replace',
         })
       );
       expect(response.body).toMatchObject({