diff --git a/packages/core/src/database/update-where.test.ts b/packages/core/src/database/update-where.test.ts
index 806b39172..b75577f3d 100644
--- a/packages/core/src/database/update-where.test.ts
+++ b/packages/core/src/database/update-where.test.ts
@@ -1,4 +1,4 @@
-import { CreateUser, Users } from '@logto/schemas';
+import { CreateUser, Users, Applications } from '@logto/schemas';
 
 import RequestError from '@/errors/RequestError';
 import { createTestPool } from '@/utils/test-utils';
@@ -35,6 +35,24 @@ describe('buildUpdateWhere()', () => {
     ).resolves.toStrictEqual(user);
   });
 
+  it('return query with jsonb partial update if input data type is jsonb', async () => {
+    const pool = createTestPool(
+      'update "applications"\nset\n"custom_client_metadata"=\ncoalesce("custom_client_metadata",\'{}\'::jsonb)|| $1\nwhere "id"=$2\nreturning *',
+      (_, [costumClientMetadata, id]) => ({
+        id: String(id),
+        costumClientMetadata: String(costumClientMetadata),
+      })
+    );
+    const updateWhere = buildUpdateWhere(pool, Applications, true);
+
+    await expect(
+      updateWhere({
+        set: { customClientMetadata: { idTokenTtl: 3600 } },
+        where: { id: 'foo' },
+      })
+    ).resolves.toStrictEqual({ id: 'foo', costumClientMetadata: '{"idTokenTtl":3600}' });
+  });
+
   it('throws an error when `undefined` found in values', async () => {
     const pool = createTestPool(
       'update "users"\nset "username"=$1\nwhere "id"=$2 and "username"=$3'
diff --git a/packages/core/src/database/update-where.ts b/packages/core/src/database/update-where.ts
index e082caf4b..13f6a5866 100644
--- a/packages/core/src/database/update-where.ts
+++ b/packages/core/src/database/update-where.ts
@@ -38,10 +38,25 @@ export const buildUpdateWhere: BuildUpdateWhere = <
   const isKeyOfSchema = isKeyOf(schema);
   const connectKeyValueWithEqualSign = (data: Partial<Schema>) =>
     Object.entries(data)
-      .map(
-        ([key, value]) =>
-          isKeyOfSchema(key) && sql`${fields[key]}=${convertToPrimitiveOrSql(key, value)}`
-      )
+      .map(([key, value]) => {
+        if (!isKeyOfSchema(key)) {
+          return;
+        }
+
+        if (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
+           * https://www.postgresql.org/docs/current/functions-json.html
+           */
+          return sql`
+            ${fields[key]}=
+              coalesce(${fields[key]},'{}'::jsonb)|| ${convertToPrimitiveOrSql(key, value)}
+          `;
+        }
+
+        return sql`${fields[key]}=${convertToPrimitiveOrSql(key, value)}`;
+      })
       .filter((value): value is Truthy<typeof value> => notFalsy(value));
 
   return async ({ set, where }: UpdateWhereData<Schema>) => {
diff --git a/packages/core/src/routes/application.ts b/packages/core/src/routes/application.ts
index 351823e49..15053e352 100644
--- a/packages/core/src/routes/application.ts
+++ b/packages/core/src/routes/application.ts
@@ -84,14 +84,9 @@ export default function applicationRoutes<T extends AuthedRouter>(router: T) {
         params: { id },
         body,
       } = ctx.guard;
-      const application = await findApplicationById(id);
 
       ctx.body = await updateApplicationById(id, {
         ...body,
-        oidcClientMetadata: buildOidcClientMetadata({
-          ...application.oidcClientMetadata,
-          ...body.oidcClientMetadata,
-        }),
       });
 
       return next();