diff --git a/packages/core/src/utils/QueryHelper.ts b/packages/core/src/utils/QueryHelper.ts
index 2d09da8d64c7..179344ad30ee 100644
--- a/packages/core/src/utils/QueryHelper.ts
+++ b/packages/core/src/utils/QueryHelper.ts
@@ -1,7 +1,7 @@
 import { Reference } from '../entity/Reference';
 import { Utils } from './Utils';
 import type { AnyEntity, Dictionary, EntityMetadata, EntityProperty, FilterDef, ObjectQuery, FilterQuery } from '../typings';
-import { ARRAY_OPERATORS, GroupOperator } from '../enums';
+import { ARRAY_OPERATORS, GroupOperator, ReferenceType } from '../enums';
 import type { Platform } from '../platforms';
 import type { MetadataStorage } from '../metadata/MetadataStorage';
 import { JsonType } from '../types';
@@ -56,7 +56,17 @@ export class QueryHelper {
     }
 
     if (meta.primaryKeys.every(pk => pk in where) && Utils.getObjectKeysSize(where) === meta.primaryKeys.length) {
-      return !GroupOperator[key as string] && Object.keys(where).every(k => !Utils.isPlainObject(where[k]) || Object.keys(where[k]).every(v => !Utils.isOperator(v, false)));
+      return !GroupOperator[key as string] && Object.keys(where).every(k => !Utils.isPlainObject(where[k]) || Object.keys(where[k]).every(v => {
+        if (Utils.isOperator(v, false)) {
+          return false;
+        }
+
+        if ([ReferenceType.ONE_TO_ONE, ReferenceType.MANY_TO_ONE].includes(meta.properties[k].reference)) {
+          return this.inlinePrimaryKeyObjects(where[k], meta.properties[k].targetMeta, metadata, v);
+        }
+
+        return true;
+      }));
     }
 
     Object.keys(where).forEach(k => {
diff --git a/packages/knex/src/query/ObjectCriteriaNode.ts b/packages/knex/src/query/ObjectCriteriaNode.ts
index f423c4ecf0b0..7beaa852538b 100644
--- a/packages/knex/src/query/ObjectCriteriaNode.ts
+++ b/packages/knex/src/query/ObjectCriteriaNode.ts
@@ -105,7 +105,16 @@ export class ObjectCriteriaNode extends CriteriaNode {
     const embeddable = this.prop.reference === ReferenceType.EMBEDDED;
     const knownKey = [ReferenceType.SCALAR, ReferenceType.MANY_TO_ONE, ReferenceType.EMBEDDED].includes(this.prop.reference) || (this.prop.reference === ReferenceType.ONE_TO_ONE && this.prop.owner);
     const operatorKeys = knownKey && Object.keys(this.payload).every(key => Utils.isOperator(key, false));
-    const primaryKeys = knownKey && Object.keys(this.payload).every(key => this.metadata.find(this.entityName)!.primaryKeys.includes(key));
+    const primaryKeys = knownKey && Object.keys(this.payload).every(key => {
+      const meta = this.metadata.find(this.entityName)!;
+      if (!meta.primaryKeys.includes(key)) {
+        return false;
+      }
+      if (!Utils.isPlainObject(this.payload[key].payload) || ![ReferenceType.ONE_TO_ONE, ReferenceType.MANY_TO_ONE].includes(meta.properties[key].reference)) {
+        return true;
+      }
+      return Object.keys(this.payload[key].payload).every(k => meta.properties[key].targetMeta!.primaryKeys.includes(k));
+    });
 
     return !primaryKeys && !nestedAlias && !operatorKeys && !embeddable;
   }
diff --git a/tests/issues/GH2648.test.ts b/tests/issues/GH2648.test.ts
new file mode 100644
index 000000000000..1d637b1bde0c
--- /dev/null
+++ b/tests/issues/GH2648.test.ts
@@ -0,0 +1,130 @@
+import { Entity, IdentifiedReference, JsonType, ManyToOne, MikroORM, OneToOne, PrimaryKey, PrimaryKeyType, Property } from '@mikro-orm/core';
+import type { SqliteDriver } from '@mikro-orm/sqlite';
+
+@Entity()
+export class A {
+
+  @PrimaryKey()
+  id!: number;
+
+  @Property({ type: 'string' })
+  test!: string;
+
+}
+
+@Entity()
+export class B1 {
+
+  [PrimaryKeyType]: number;
+  @ManyToOne({ entity: () => A, primary: true, wrappedReference: true })
+  a!: IdentifiedReference<A>;
+
+}
+
+@Entity()
+export class B2 {
+
+  @PrimaryKey()
+  id!: number;
+
+  [PrimaryKeyType]: number;
+  @OneToOne({ entity: () => A, primary: true, wrappedReference: true })
+  a!: IdentifiedReference<A>;
+
+}
+
+@Entity()
+export class B3 {
+
+  [PrimaryKeyType]: number;
+  @OneToOne({ entity: () => A, primary: true, wrappedReference: true })
+  a!: IdentifiedReference<A>;
+
+}
+
+@Entity()
+export class B4 {
+
+  @PrimaryKey()
+  id!: number;
+
+  [PrimaryKeyType]: number;
+  @OneToOne({ entity: () => A, primary: true, wrappedReference: true })
+  a!: IdentifiedReference<A>;
+
+}
+
+@Entity()
+export class C {
+
+  @PrimaryKey({ type: Number })
+  id!: number;
+
+  @ManyToOne({ entity: () => B1, wrappedReference: true })
+  b1!: IdentifiedReference<B1>;
+
+  @ManyToOne({ entity: () => B2, wrappedReference: true })
+  b2!: IdentifiedReference<B2>;
+
+  @ManyToOne({ entity: () => B3, wrappedReference: true })
+  b3!: IdentifiedReference<B3>;
+
+  @ManyToOne({ entity: () => B4, wrappedReference: true })
+  b4!: IdentifiedReference<B4>;
+
+}
+
+interface Test {
+  t1: string;
+  t2: string;
+}
+
+@Entity()
+export class D {
+
+  @PrimaryKey({ type: JsonType })
+  id!: Test;
+
+}
+
+describe('GH issue 2648', () => {
+
+  let orm: MikroORM<SqliteDriver>;
+
+  beforeAll(async () => {
+    orm = await MikroORM.init({
+      entities: [A, B1, B2, B3, B4, C, D],
+      dbName: ':memory:',
+      type: 'sqlite',
+    });
+    await orm.getSchemaGenerator().createSchema();
+  });
+
+  afterAll(() => orm.close(true));
+
+  test('JSON as pk', async () => {
+    const r = await orm.em.findOne(D, { id: { t1: 'a', t2: 'b' } });
+    expect(r).toBeNull();
+  });
+
+  test('fk as pk with ManyToOne', async () => {
+    const r = await orm.em.findOne(C, { b1: { a: { test: 'test' } } });
+    expect(r).toBeNull();
+  });
+
+  test('fk as pk with ManyToOne and with additional primary key', async () => {
+    const r = await orm.em.findOne(C, { b2: { a: { test: 'test' } } });
+    expect(r).toBeNull();
+  });
+
+  test('fk as pk with OneToOne', async () => {
+    const r = await orm.em.findOne(C, { b3: { a: { test: 'test' } } });
+    expect(r).toBeNull();
+  });
+
+  test('fk as pk with OneToOne and with additional primary key', async () => {
+    const r = await orm.em.findOne(C, { b4: { a: { test: 'test' } } });
+    expect(r).toBeNull();
+  });
+
+});