During the missions, whatever movie you prefer, Tony Stark spend more than 5 hours per mission (given the time passed and the sequence of the movies) in the suit. I was wondering if he has physiologic needs (such as poop or pee) and having the armor, what could he do?
Yes, he can. Specifically, he can urinate.
In the second part of Iron Man (2010), Tony is celebrating his birthday with almost 90% of paladium in his body and decided to celebrate like the last party of his life and put his suit for the party. When he's making a speech in front of his guests, he says that many people ask often how to go to the bathroom with the armor and make a joke.
You just pee in your suit!
Tony replied Pepper:
I know but it has (the suit) a filter system. You could drink that water (ex-urine).