diff --git a/packages/core/src/unit-of-work/ChangeSetPersister.ts b/packages/core/src/unit-of-work/ChangeSetPersister.ts
index 35e71845cf5f..0092553dc8fc 100644
--- a/packages/core/src/unit-of-work/ChangeSetPersister.ts
+++ b/packages/core/src/unit-of-work/ChangeSetPersister.ts
@@ -71,7 +71,7 @@ export class ChangeSetPersister {
       const chunk = changeSets.slice(i, i + size);
       const pks = chunk.map(cs => cs.getPrimaryKey());
       options = this.propagateSchemaFromMetadata(meta, options);
-      await this.driver.nativeDelete(meta.className, { [pk]: { $in: pks } } as FilterQuery<T>, options);
+      await this.driver.nativeDelete(meta.root.className, { [pk]: { $in: pks } } as FilterQuery<T>, options);
     }
   }
 
diff --git a/tests/features/single-table-inheritance/GH5303.test.ts b/tests/features/single-table-inheritance/GH5303.test.ts
new file mode 100644
index 000000000000..3892440c0e73
--- /dev/null
+++ b/tests/features/single-table-inheritance/GH5303.test.ts
@@ -0,0 +1,115 @@
+import { Cascade, Collection, Entity, ManyToOne, MikroORM, OneToMany, PrimaryKey, Property } from '@mikro-orm/sqlite';
+
+@Entity()
+class User {
+
+  @PrimaryKey()
+  id!: number;
+
+  @OneToMany({
+    entity: () => CoverPicture,
+    mappedBy: 'cover_user',
+    orphanRemoval: true,
+    eager: true,
+    cascade: [Cascade.ALL],
+  })
+  cover_pictures: Collection<CoverPicture> = new Collection<CoverPicture>(this);
+
+  @OneToMany({
+    entity: () => ProfilePicture,
+    mappedBy: 'profile_user',
+    orphanRemoval: true,
+    eager: true,
+    cascade: [Cascade.ALL],
+  })
+  profile_pictures: Collection<ProfilePicture> = new Collection<ProfilePicture>(this);
+
+}
+
+@Entity({ abstract: true, discriminatorColumn: 'type' })
+abstract class BasePicture {
+
+  @PrimaryKey()
+  id!: number;
+
+  @Property({ type: 'string', nullable: false })
+  path: string;
+
+  constructor(path: string) {
+    this.path = path;
+  }
+
+}
+
+@Entity({ discriminatorValue: 'cover' })
+class CoverPicture extends BasePicture {
+
+  @ManyToOne({ entity: () => User })
+  cover_user: User;
+
+  constructor(path: string, user: User) {
+    super(path);
+    this.cover_user = user;
+  }
+
+}
+
+@Entity({ discriminatorValue: 'profile' })
+class ProfilePicture extends BasePicture {
+
+  @ManyToOne({ entity: () => User })
+  profile_user: User;
+
+  constructor(path: string, user: User) {
+    super(path);
+    this.profile_user = user;
+  }
+
+}
+
+let orm: MikroORM;
+
+beforeAll(async () => {
+  orm = await MikroORM.init({
+    dbName: ':memory:',
+    entities: [User, BasePicture, CoverPicture, ProfilePicture],
+  });
+  await orm.schema.refreshDatabase();
+});
+
+afterAll(async () => {
+  await orm.close(true);
+});
+
+test('user should be able to create/update pictures', async () => {
+  let user = new User();
+  orm.em.create(User, user);
+  await orm.em.persist(user).flush();
+  orm.em.clear();
+
+  user = await orm.em.findOneOrFail(User, { id: user.id });
+  user.cover_pictures.add(new CoverPicture('/path/1', user));
+  user.profile_pictures.add(new ProfilePicture('/path/2', user));
+  await orm.em.persist(user).flush();
+  orm.em.clear();
+
+  user = await orm.em.findOneOrFail(User, { id: user.id });
+  expect(user.cover_pictures.length).toBe(1);
+  expect(user.profile_pictures.length).toBe(1);
+
+  // update pictures
+  user.cover_pictures.removeAll();
+  user.profile_pictures.removeAll();
+
+  user.cover_pictures.add(new CoverPicture('/path/3', user));
+  user.profile_pictures.add(new ProfilePicture('/path/4', user));
+
+  await orm.em.persist(user).flush();
+  orm.em.clear();
+
+  user = await orm.em.findOneOrFail(User, { id: user.id });
+  expect(user.cover_pictures.length).toBe(1);
+  expect(user.profile_pictures.length).toBe(1);
+  expect(user.cover_pictures[0].path).toBe('/path/3');
+  expect(user.profile_pictures[0].path).toBe('/path/4');
+});