diff --git a/packages/core/src/metadata/MetadataDiscovery.ts b/packages/core/src/metadata/MetadataDiscovery.ts
index 4dc92a8a05cc..0002c22c856b 100644
--- a/packages/core/src/metadata/MetadataDiscovery.ts
+++ b/packages/core/src/metadata/MetadataDiscovery.ts
@@ -376,10 +376,15 @@ export class MetadataDiscovery {
     const meta2 = this.metadata.get(prop.type);
     Utils.defaultValue(prop, 'fixedOrder', !!prop.fixedOrderColumn);
     const pivotMeta = this.metadata.find(prop.pivotEntity);
+    const pks = Object.values(pivotMeta?.properties ?? {}).filter(p => p.primary);
 
-    if (pivotMeta) {
+    if (pivotMeta && pks.length === 2) {
+      const owner = prop.mappedBy ? meta2.properties[prop.mappedBy] : prop;
+      const [first, second] = this.ensureCorrectFKOrderInPivotEntity(pivotMeta, owner);
       pivotMeta.pivotTable = true;
       prop.pivotTable = pivotMeta.tableName;
+      prop.joinColumns = first.fieldNames;
+      prop.inverseJoinColumns = second.fieldNames;
     }
 
     if (!prop.pivotTable && prop.owner && this.platform.usesPivotTable()) {
@@ -491,8 +496,8 @@ export class MetadataDiscovery {
     });
   }
 
-  private ensureCorrectFKOrderInPivotEntity(meta: EntityMetadata, owner: EntityProperty): void {
-    const [first, second] = meta.relations;
+  private ensureCorrectFKOrderInPivotEntity(meta: EntityMetadata, owner: EntityProperty): [EntityProperty, EntityProperty] {
+    let [first, second] = Object.values(meta.properties).filter(p => p.primary);
 
     // wrong FK order, first FK needs to point to the owning side
     // (note that we can detect this only if the FKs target different types)
@@ -500,7 +505,10 @@ export class MetadataDiscovery {
       delete meta.properties[first.name];
       meta.removeProperty(first.name, false);
       meta.addProperty(first);
+      [first, second] = [second, first];
     }
+
+    return [first, second];
   }
 
   private async definePivotTableEntity(meta: EntityMetadata, prop: EntityProperty): Promise<EntityMetadata> {
diff --git a/tests/features/composite-keys/__snapshots__/custom-pivot-entity-with-sti.test.ts.snap b/tests/features/composite-keys/__snapshots__/custom-pivot-entity-with-sti.test.ts.snap
new file mode 100644
index 000000000000..b41e5a75e2f7
--- /dev/null
+++ b/tests/features/composite-keys/__snapshots__/custom-pivot-entity-with-sti.test.ts.snap
@@ -0,0 +1,17 @@
+// Jest Snapshot v1, https://goo.gl/fbAQLP
+
+exports[`schema 1`] = `
+"pragma foreign_keys = off;
+
+create table \`task\` (\`id\` integer not null primary key autoincrement);
+
+create table \`user\` (\`id\` integer not null primary key autoincrement, \`role\` text not null default 'CREATOR');
+create index \`user_role_index\` on \`user\` (\`role\`);
+
+create table \`creators_on_tasks\` (\`creator_id\` integer not null, \`task_id\` integer not null, constraint \`creators_on_tasks_creator_id_foreign\` foreign key(\`creator_id\`) references \`user\`(\`id\`) on update cascade, constraint \`creators_on_tasks_task_id_foreign\` foreign key(\`task_id\`) references \`task\`(\`id\`) on update cascade, primary key (\`creator_id\`, \`task_id\`));
+create index \`creators_on_tasks_creator_id_index\` on \`creators_on_tasks\` (\`creator_id\`);
+create index \`creators_on_tasks_task_id_index\` on \`creators_on_tasks\` (\`task_id\`);
+
+pragma foreign_keys = on;
+"
+`;
diff --git a/tests/features/composite-keys/custom-pivot-entity-with-sti.test.ts b/tests/features/composite-keys/custom-pivot-entity-with-sti.test.ts
new file mode 100644
index 000000000000..72e2996aacf8
--- /dev/null
+++ b/tests/features/composite-keys/custom-pivot-entity-with-sti.test.ts
@@ -0,0 +1,86 @@
+import { Collection, Entity, ManyToMany, ManyToOne, MikroORM, PrimaryKey, Property } from '@mikro-orm/core';
+
+@Entity({
+  discriminatorColumn: 'role',
+  discriminatorMap: {
+    CREATOR: 'Creator',
+  },
+})
+class User {
+
+  @PrimaryKey()
+  id!: number;
+
+  @Property()
+  role: 'CREATOR' = 'CREATOR' as const;
+
+}
+
+@Entity()
+class Creator extends User {
+
+  // eslint-disable-next-line @typescript-eslint/no-use-before-define
+  @ManyToMany({ entity: () => Task, pivotEntity: () => CreatorsOnTasks })
+  tasks = new Collection<Task>(this);
+
+}
+
+@Entity()
+class Task {
+
+  @PrimaryKey()
+  id!: number;
+
+  @ManyToMany(() => Creator, c => c.tasks)
+  creators = new Collection<Creator>(this);
+
+}
+
+@Entity()
+class CreatorsOnTasks {
+
+  @ManyToOne({ primary: true, entity: () => Creator })
+  creator!: Creator;
+
+  @ManyToOne({ primary: true, entity: () => Task })
+  task!: Task;
+
+}
+
+let orm: MikroORM;
+
+beforeAll(async () => {
+  orm = await MikroORM.init({
+    entities: [User, Creator, CreatorsOnTasks, Task],
+    dbName: ':memory:',
+    type: 'sqlite',
+  });
+  await orm.schema.createSchema();
+});
+
+afterAll(async () => await orm.close(true));
+
+beforeEach(() => orm.schema.clearDatabase());
+
+test('schema', async () => {
+  const sql = await orm.schema.getCreateSchemaSQL();
+  expect(sql).toMatchSnapshot();
+});
+
+async function createEntities() {
+  const task = new Task();
+  const creator = new Creator();
+  task.creators.add(creator);
+  await orm.em.fork().persistAndFlush(task);
+
+  return { task };
+}
+
+test('should insert', async () => {
+  await expect(createEntities()).resolves.not.toThrow();
+});
+
+test('should not findOne and populate m:n relation', async () => {
+  const { task } = await createEntities();
+  await expect(orm.em.findOne(Task, { id: task.id }, { populate: ['creators'] })).resolves.not.toThrow();
+});