Depends. He is indestructible and, as far as I know, not a renowned chef. Cooking with ingredients that you actually put in food should be totally safe for him.

He might be able to find some kind of exotic alien substance that could cause some physical pain, but at that point, is he really cooking? Or just adding something painful to food?

Sidenote, he could probably find some kind of kryptonite that would disable his powers for a meal.