diff --git a/packages/knex/src/query/QueryBuilder.ts b/packages/knex/src/query/QueryBuilder.ts
index 91e81b951b43..46c9ecf2f5b3 100644
--- a/packages/knex/src/query/QueryBuilder.ts
+++ b/packages/knex/src/query/QueryBuilder.ts
@@ -576,6 +576,10 @@ export class QueryBuilder<T extends AnyEntity<T> = AnyEntity> {
     const tableName = this.helper.getTableName(this.entityName) + (this.finalized && this.helper.isTableNameAliasRequired(this.type) ? ` as ${this.alias}` : '');
     const qb = this.knex(tableName);
 
+    if (this._schema) {
+      qb.withSchema(this._schema);
+    }
+
     if (this.context) {
       qb.transacting(this.context);
     }
diff --git a/tests/features/multiple-schemas/different-schema-from-config.postgres.test.ts b/tests/features/multiple-schemas/different-schema-from-config.postgres.test.ts
index 7d674222a561..f1217aad872d 100644
--- a/tests/features/multiple-schemas/different-schema-from-config.postgres.test.ts
+++ b/tests/features/multiple-schemas/different-schema-from-config.postgres.test.ts
@@ -1,8 +1,8 @@
-import { Entity, MikroORM, PrimaryKey, Property, wrap } from '@mikro-orm/core';
+import { Collection, Entity, ManyToMany, MikroORM, PrimaryKey, Property, wrap } from '@mikro-orm/core';
 import type { PostgreSqlDriver } from '@mikro-orm/postgresql';
 
 @Entity()
-export class CoreEntity {
+export class BookTag {
 
   @PrimaryKey()
   id!: number;
@@ -16,6 +16,24 @@ export class CoreEntity {
 
 }
 
+@Entity()
+export class Book {
+
+  @PrimaryKey()
+  id!: number;
+
+  @Property()
+  name: string;
+
+  @ManyToMany(() => BookTag)
+  tags = new Collection<BookTag>(this);
+
+  constructor(name: string) {
+    this.name = name;
+  }
+
+}
+
 describe('different schema from config', () => {
 
   let orm: MikroORM<PostgreSqlDriver>;
@@ -23,9 +41,9 @@ describe('different schema from config', () => {
   beforeAll(async () => {
     orm = await MikroORM.init({
       type: 'postgresql',
+      entities: [Book, BookTag],
       dbName: 'mikro_orm_test_gh_2740',
       schema: 'privateschema',
-      entities: [CoreEntity],
     });
     await orm.getSchemaGenerator().refreshDatabase();
   });
@@ -35,31 +53,43 @@ describe('different schema from config', () => {
   });
 
   beforeEach(async () => {
-    await orm.em.nativeDelete(CoreEntity, {});
+    await orm.em.nativeDelete('book_tags', {});
+    await orm.em.nativeDelete(BookTag, {});
+    await orm.em.nativeDelete(Book, {});
     orm.em.clear();
   });
 
   it('should respect the global schema config', async () => {
-    const entity = new CoreEntity('n');
+    const entity = new Book('n');
+    entity.tags.add(new BookTag('t'));
     await orm.em.persistAndFlush(entity);
     expect(entity.id).toBeDefined();
     orm.em.clear();
 
-    const e = await orm.em.findOne(CoreEntity, entity);
+    const e = await orm.em.findOne(Book, entity);
     expect(e).not.toBeNull();
     expect(wrap(e).getSchema()).toBe('privateschema');
+    e!.tags.set([new BookTag('t2')]);
+    await orm.em.flush();
   });
 
   it('should respect the global schema config (multi insert)', async () => {
-    await orm.em.fork().persistAndFlush([new CoreEntity('n1'), new CoreEntity('n2'), new CoreEntity('n3')]);
+    const books = [new Book('n1'), new Book('n2'), new Book('n3')];
+    books[0].tags.add(new BookTag('t1'));
+    books[1].tags.add(new BookTag('t2'));
+    books[2].tags.add(new BookTag('t3'));
+    await orm.em.fork().persistAndFlush(books);
 
-    const res = await orm.em.find(CoreEntity, {});
+    const res = await orm.em.find(Book, {}, { populate: ['tags'] });
     expect(res).toHaveLength(3);
     expect(wrap(res[0]).getSchema()).toBe('privateschema');
     expect(wrap(res[1]).getSchema()).toBe('privateschema');
     expect(wrap(res[2]).getSchema()).toBe('privateschema');
 
     res.forEach(row => row.name = `name ${row.id}`);
+    res[0].tags.set([new BookTag('t21')]);
+    res[1].tags.set([new BookTag('t22')]);
+    res[2].tags.set([new BookTag('t23')]);
     await orm.em.flush();
   });