Beat the game with the hidden ending but never figured this one out. How do you open it?

Are you talking about the door on the way out after defeating the Krotite God Boss, that has an empty pearl socket next to it? You need to go to the right exit on the same map and use your energy form to toss a seed on the plant there. It will give you a pearl to open the door.

I don't remember, maybe I'll replay it sometime.