Preheat oven to 375 degrees F (190 degrees C). Spray a 12-cup muffin tin with cooking spray.
Flatten croissants out using a rolling pin on a work surface; cut into 4-inch squares. Press croissant squares in the prepared muffin cups.
Beat eggs, milk, onion powder, nutmeg, salt, and black pepper together in a bowl. Stir in three-cheese blend and spinach. Spoon egg mixture into croissant squares until about 2/3 full.
Bake in the preheated oven until browned and egg is set in the middle, about 20 minutes.