diff --git a/packages/core/src/unit-of-work/UnitOfWork.ts b/packages/core/src/unit-of-work/UnitOfWork.ts
index 681881a4cf54..1086df852f2a 100644
--- a/packages/core/src/unit-of-work/UnitOfWork.ts
+++ b/packages/core/src/unit-of-work/UnitOfWork.ts
@@ -101,7 +101,7 @@ export class UnitOfWork {
 
       wrapped.__meta.relations.forEach(prop => {
         if (Utils.isPlainObject(data[prop.name as string])) {
-          data[prop.name as string] = Utils.getPrimaryKeyValues(data[prop.name as string], wrapped.__meta.primaryKeys, true);
+          data[prop.name as string] = Utils.getPrimaryKeyValues(data[prop.name as string], prop.targetMeta!.primaryKeys, true);
         }
       });
       wrapped.__originalEntityData = data;
diff --git a/tests/features/unit-of-work/GH4129.test.ts b/tests/features/unit-of-work/GH4129.test.ts
new file mode 100644
index 000000000000..9f7f8c98270e
--- /dev/null
+++ b/tests/features/unit-of-work/GH4129.test.ts
@@ -0,0 +1,109 @@
+import { Collection, Entity, LoadStrategy, ManyToOne, OneToMany, PrimaryKey, Property, SimpleLogger } from '@mikro-orm/core';
+import { MikroORM } from '@mikro-orm/sqlite';
+import { mockLogger } from '../../helpers';
+
+@Entity()
+class Channel {
+
+  @PrimaryKey()
+  id!: number;
+
+  @Property()
+  name!: string;
+
+  @OneToMany(() => DeviceChannel, item => item.channel, { orphanRemoval: true })
+  links = new Collection<DeviceChannel>(this);
+
+}
+
+@Entity()
+class Device {
+
+  @PrimaryKey()
+  id!: number;
+
+  @Property()
+  serial!: string;
+
+  @OneToMany(() => DeviceChannel, item => item.device, { orphanRemoval: true })
+  links = new Collection<DeviceChannel>(this);
+
+}
+
+@Entity()
+class DeviceChannel {
+
+  @ManyToOne({ entity: () => Device, primary: true })
+  device!: Device;
+
+  @ManyToOne({ entity: () => Channel, primary: true })
+  channel!: Channel;
+
+  @Property()
+  lastTime!: Date;
+
+}
+
+let orm: MikroORM;
+
+beforeAll(async () => {
+  orm = await MikroORM.init({
+    entities: [Device, Channel, DeviceChannel],
+    dbName: ':memory:',
+    loggerFactory: options => new SimpleLogger(options),
+    loadStrategy: LoadStrategy.JOINED,
+  });
+  await orm.schema.refreshDatabase();
+});
+
+afterAll(async () => {
+  await orm.close(true);
+});
+
+beforeEach(async () => {
+  await orm.schema.clearDatabase();
+
+  const chn = orm.em.create(Channel, { id: 1, name: 'ChannelOne', links: [] });
+  const dev1 = orm.em.create(Device, { id: 2, serial: 'DeviceOne', links: [] });
+  const link1 = orm.em.create(DeviceChannel, { device: dev1, channel: chn, lastTime: new Date() });
+  chn.links.add(link1);
+
+  await orm.em.flush();
+  orm.em.clear();
+});
+
+test('GH 4129 (1/3)', async () => {
+  const channel = await orm.em.findOneOrFail(Channel, { name: 'ChannelOne' }, { populate: ['links'] });
+
+  for (const link of channel.links) {
+    link.lastTime = new Date(1678803173316);
+  }
+
+  const mock = mockLogger(orm);
+  await orm.em.flush();
+  expect(mock.mock.calls[1][0]).toBe('[query] update `device_channel` set `last_time` = 1678803173316 where (`device_id`, `channel_id`) in ((2, 1))');
+});
+
+test('GH 4129 (2/3)', async () => {
+  const channel = await orm.em.findOneOrFail(Channel, { name: 'ChannelOne' }, { populate: ['links.device', 'links.channel'] });
+
+  for (const link of channel.links) {
+    link.lastTime = new Date(1678803173316);
+  }
+
+  const mock = mockLogger(orm);
+  await orm.em.flush();
+  expect(mock.mock.calls[1][0]).toBe('[query] update `device_channel` set `last_time` = 1678803173316 where (`device_id`, `channel_id`) in ((2, 1))');
+});
+
+test('GH 4129 (3/3)', async () => {
+  const channel = await orm.em.findOneOrFail(Channel, { name: 'ChannelOne' }, { populate: ['links.device'] });
+
+  for (const link of channel.links) {
+    link.lastTime = new Date(1678803173316);
+  }
+
+  const mock = mockLogger(orm);
+  await orm.em.flush();
+  expect(mock.mock.calls[1][0]).toBe('[query] update `device_channel` set `last_time` = 1678803173316 where (`device_id`, `channel_id`) in ((2, 1))');
+});