Spray each tin in a 12 cup muffin pan with cooking spray and preheat your oven to 400 degrees. Cook sausage, onion, and crushed red pepper in a large skillet over medium heat, breaking up as you go, until sausage is cooked through.
Divide your cooked sausage mixture evenly among the prepared muffin tin cups.
Meanwhile, whisk together eggs, milk, paprika, salt, and pepper until fully combined and bubbly, then pour egg mixture evenly into each muffin tin on top of the sausage.
Top each egg muffin with shredded cheese, then bake at 400 degrees for 20 minutes.
Don't worry that you're not filling the cups all the way; the breakfast muffins do rise quite a bit (see photo above) and you'll want to leave room for them to expand.