Preheat oven to 350 degrees F (175 degrees C). Spray 12 muffin cups with cooking spray.
Lay 2 ham slices in each muffin cup, overlapping the slices and pressing up the sides to take the shape of the cup.
Beat eggs in a bowl; season with salt and pepper. Add onion and beat well. Fill each ham cup 3/4 full with egg mixture; top each with Cheddar cheese and mozzarella cheese.
Bake in the preheated oven until egg is cooked through, 15 to 20 minutes. Cool for 5 minutes before serving.
