1Preheat oven to 375 degrees F (190 degrees C). Prepare 12 muffin cups with cooking spray.
2Arrange bacon on a microwave-safe plate. Cook bacon in microwave for 75 seconds.
3Place a slice of bacon into each muffin cup so that the bacon lines the edges of the cup.
4Beat eggs and milk together in a bowl; ladle into muffin cups. Top 4 of the egg portions with 1 tablespoon each of the green onion, 4 with 1 tablespoon each jalapeno pepper, and 4 each with 1 tablespoon roasted red pepper.
5Bake in preheated oven until only slightly moist on top, about 20 minutes. Season the muffins with salt and pepper; top with Cheddar cheese. Continue baking until the cheese melts, about 5 minutes more.