diff --git a/packages/reflection/src/TsMorphMetadataProvider.ts b/packages/reflection/src/TsMorphMetadataProvider.ts
index 377c89eefd41..7343a266af96 100644
--- a/packages/reflection/src/TsMorphMetadataProvider.ts
+++ b/packages/reflection/src/TsMorphMetadataProvider.ts
@@ -1,7 +1,7 @@
 import type { PropertyDeclaration, SourceFile } from 'ts-morph';
-import { Project, ModuleKind } from 'ts-morph';
+import { ModuleKind, Project } from 'ts-morph';
 import type { EntityMetadata, EntityProperty } from '@mikro-orm/core';
-import { MetadataError, MetadataProvider, MetadataStorage, Utils } from '@mikro-orm/core';
+import { MetadataError, MetadataProvider, MetadataStorage, ReferenceType, Utils } from '@mikro-orm/core';
 
 export class TsMorphMetadataProvider extends MetadataProvider {
 
@@ -123,7 +123,7 @@ export class TsMorphMetadataProvider extends MetadataProvider {
       .replace(/\((.*)\)/, '$1');   // unwrap union types
 
     // keep the array suffix in the type, it is needed in few places in discovery and comparator (`prop.array` is used only for enum arrays)
-    if (prop.array && !type.includes(' | ')) {
+    if (prop.array && !type.includes(' | ') && prop.reference === ReferenceType.SCALAR) {
       type += '[]';
     }
 
diff --git a/tests/features/embeddables/GH3690.test.ts b/tests/features/embeddables/GH3690.test.ts
new file mode 100644
index 000000000000..8645d0ab6de2
--- /dev/null
+++ b/tests/features/embeddables/GH3690.test.ts
@@ -0,0 +1,68 @@
+import { Embeddable, Embedded, Entity, PrimaryKey, Property, OneToOne, Ref } from '@mikro-orm/core';
+import { MikroORM } from '@mikro-orm/sqlite';
+import { TsMorphMetadataProvider } from '@mikro-orm/reflection';
+
+@Embeddable()
+export class PTE {
+
+  @Property()
+  name!: string;
+
+}
+
+@Entity()
+export class BPE {
+
+  @PrimaryKey()
+  id!: number;
+
+  @Embedded({ object: true })
+  titles!: PTE[];
+
+  @OneToOne(() => P, p => p.bp, { orphanRemoval: true })
+  p!: Ref<P> | null;
+
+}
+
+@Entity()
+export class P {
+
+  @PrimaryKey()
+  id!: number;
+
+  @OneToOne(() => BPE, { orphanRemoval: true })
+  bp!: Ref<BPE> | null;
+
+}
+
+let orm: MikroORM;
+
+beforeAll(async () => {
+  orm = await MikroORM.init({
+    entities: [P, PTE],
+    dbName: ':memory:',
+    metadataProvider: TsMorphMetadataProvider,
+    cache: { enabled: false },
+  });
+  await orm.schema.createSchema();
+});
+
+afterAll(async () => {
+  await orm.close(true);
+});
+
+test('GH issue 3690', async () => {
+  const e = orm.em.create(P, {
+    bp: {
+      titles: [{ name: 't1' }, { name: 't2' }],
+    },
+  });
+  await orm.em.flush();
+  orm.em.clear();
+
+  const e1 = await orm.em.findOneOrFail(P, e, { populate: ['bp'] });
+  expect(e1.bp?.$.titles).toEqual([
+    { name: 't1' },
+    { name: 't2' },
+  ]);
+});