Whisk evaporated milk, eggs, and baking powder together in a bowl.
Spread half the chili on the bottom of a casserole dish. Spread pepperjack cheese and mozzarella cheese over the chili. Spread remaining half the chili on top of the cheese. Spread Cheddar cheese over chili. Pour egg mixture over Cheddar cheese.
Bake in the preheated oven until eggs are set and cheese is melted and bubbling, 55 to 57 minutes.