diff --git a/packages/core/src/unit-of-work/UnitOfWork.ts b/packages/core/src/unit-of-work/UnitOfWork.ts
index a038ef6806b8..8cea779a308f 100644
--- a/packages/core/src/unit-of-work/UnitOfWork.ts
+++ b/packages/core/src/unit-of-work/UnitOfWork.ts
@@ -46,7 +46,6 @@ export class UnitOfWork {
   merge<T extends object>(entity: T, visited?: Set<AnyEntity>): void {
     const wrapped = helper(entity);
     wrapped.__em = this.em;
-    wrapped.__populated = true;
 
     if (!wrapped.hasPrimaryKey()) {
       return;
@@ -59,7 +58,6 @@ export class UnitOfWork {
     }
 
     this.identityMap.store(entity);
-    wrapped.__populated = true;
 
     // if visited is available, we are cascading, and need to be careful when resetting the entity data
     // as there can be some entity with already changed state that is not yet flushed
diff --git a/tests/issues/GH3812.test.ts b/tests/issues/GH3812.test.ts
new file mode 100644
index 000000000000..01ac55468c42
--- /dev/null
+++ b/tests/issues/GH3812.test.ts
@@ -0,0 +1,188 @@
+import {
+  Collection,
+  Entity,
+  ManyToOne,
+  OneToMany,
+  DateType,
+  PrimaryKey,
+  Property,
+  Enum,
+  wrap,
+} from '@mikro-orm/core';
+import { MikroORM } from '@mikro-orm/sqlite';
+import { v4 } from 'uuid';
+
+export abstract class BaseEntity {
+
+  @PrimaryKey()
+  id: string = v4();
+
+  @Property()
+  createdAt: Date = new Date();
+
+  @Property({ onUpdate: () => new Date() })
+  updatedAt: Date = new Date();
+
+  @Property({ nullable: true })
+  deletedAt?: Date | null;
+
+}
+
+export enum StepType {
+  ASSY = 'ASSY',
+  INSP = 'INSP',
+  TEST = 'TEST',
+  PTG = 'PTG',
+}
+
+@Entity()
+export class Step extends BaseEntity {
+
+  @Property()
+  name!: string;
+
+  @Property()
+  number!: string;
+
+  @Property()
+  order!: number;
+
+  @Enum(() => StepType)
+  type!: StepType;
+
+}
+
+@Entity()
+export class SerialNumber extends BaseEntity {
+
+  @Property()
+  serialNumber!: number;
+
+  @OneToMany(() => Log, log => log.serialNumber)
+  logs = new Collection<Log>(this);
+
+}
+
+@Entity()
+export class Log extends BaseEntity {
+
+  @ManyToOne(() => SerialNumber)
+  serialNumber!: SerialNumber;
+
+  @ManyToOne()
+  step?: Step;
+
+  @Property({ type: DateType, nullable: true })
+  operationDate?: Date;
+
+  @Property({ default: false })
+  current: boolean = false;
+
+  @Property({ default: false })
+  returned: boolean = false;
+
+}
+
+let orm: MikroORM;
+
+beforeAll(async () => {
+  orm = await MikroORM.init({
+    entities: [Step, SerialNumber, Log],
+    dbName: `:memory:`,
+  });
+
+  await orm.schema.refreshDatabase();
+});
+
+afterAll(() => orm.close(true));
+
+test('GH 3812', async () => {
+  const user = orm.em.create(SerialNumber, {
+    id: '559fccf7-11f0-4e5a-8e15-ae29b98ddeb3',
+    createdAt: '2022-11-30T15:54:51.000Z',
+    updatedAt: '2022-11-30T15:54:51.000Z',
+    deletedAt: null,
+    serialNumber: 1231,
+    logs: [
+      {
+        id: 'a73827bc-70aa-4a2b-aa9f-055fc387a022',
+        createdAt: '2022-11-30T15:55:06.000Z',
+        updatedAt: '2022-11-30T15:55:06.000Z',
+        deletedAt: null,
+        step: {
+          id: '1728c421-cf23-4618-9518-e12c385a39ff',
+          createdAt: '2022-11-30T14:26:16.000Z',
+          updatedAt: '2022-11-30T14:26:16.000Z',
+          deletedAt: null,
+          name: 'ASSY',
+          number: '3',
+          order: 0,
+          type: StepType.ASSY,
+        },
+        operationDate: null,
+        current: true,
+        returned: true,
+        serialNumber: '559fccf7-11f0-4e5a-8e15-ae29b98ddeb3',
+      },
+      {
+        id: '728fc9bb-c44a-4310-a397-7a4a2f4620c2',
+        createdAt: '2022-11-30T15:54:53.000Z',
+        updatedAt: '2022-11-30T15:55:06.000Z',
+        deletedAt: '2022-11-30T15:55:06.000Z',
+        step: {
+          id: '1728c421-cf23-4618-9518-e12c385a39ff',
+          createdAt: '2022-11-30T14:26:16.000Z',
+          updatedAt: '2022-11-30T14:26:16.000Z',
+          deletedAt: null,
+          name: 'ASSY',
+          number: '3',
+          order: 0,
+          type: StepType.ASSY,
+        },
+        operationDate: '2022-11-30',
+        current: false,
+        returned: false,
+        serialNumber: '559fccf7-11f0-4e5a-8e15-ae29b98ddeb3',
+      },
+      {
+        id: 'f29aa5d1-6036-4e00-938f-483581b72184',
+        createdAt: '2022-11-30T15:55:04.000Z',
+        updatedAt: '2022-11-30T15:55:06.000Z',
+        deletedAt: null,
+        step: {
+          id: '09b64d55-d583-44ed-8407-65968a150057',
+          createdAt: '2022-11-30T14:26:16.000Z',
+          updatedAt: '2022-11-30T14:26:16.000Z',
+          deletedAt: null,
+          name: 'ASSY',
+          number: '50',
+          order: 1,
+          type: StepType.ASSY,
+        },
+        operationDate: '2022-11-30',
+        current: false,
+        returned: false,
+        serialNumber: '559fccf7-11f0-4e5a-8e15-ae29b98ddeb3',
+      },
+    ],
+  });
+  await orm.em.persistAndFlush(user);
+  orm.em.clear();
+
+  // with EM
+  const res1 = await orm.em.find(SerialNumber, {}, { populate: ['logs.step'] });
+  expect(res1).toHaveLength(1);
+  expect(wrap(res1[0]).toJSON().logs[0].serialNumber).toBe('559fccf7-11f0-4e5a-8e15-ae29b98ddeb3');
+
+  orm.em.clear();
+
+  // with QB
+  const res2 = await orm.em
+    .createQueryBuilder(SerialNumber, 'sn')
+    .select('*')
+    .leftJoinAndSelect('sn.logs', 'l')
+    .leftJoinAndSelect('l.step', 's')
+    .getResultList();
+  expect(res2).toHaveLength(1);
+  expect(wrap(res2[0]).toJSON().logs[0].serialNumber).toBe('559fccf7-11f0-4e5a-8e15-ae29b98ddeb3');
+});