I'm in my office now. Mr.Koike, my boss, is standing at the door and says "May I come in?"
Is it acceptable to say "Yes, you may." in this situation?
I think I'd most likely say "Yes, please." because he's my boss. Is "Yes, please." OK in this context?
No. I mean that your suggested response of "Yes please" is not very natural. I suggest that you say "Yes, please do" to your boss when he asks if he may come in.