Set an oven rack about 6 inches from the heat source and preheat the oven's broiler to high broil. Preheat a mini waffle iron. Line a baking sheet with aluminum foil.
Combine ½ cup mozzarella cheese, egg, almond flour, oregano, basil, garlic powder, and red pepper flakes in a bowl.
Pour ½ of the batter onto the preheated waffle iron, spreading out with a spoon. Close the waffle iron, and cook until the steaming stops and the chaffle is well browned, 3 to 4 minutes. Transfer chaffle to the prepared baking sheet and repeat with remaining batter.
Divide marinara sauce between the 2 chaffles, sprinkle with remaining mozzarella, place pepperoni on top, and sprinkle with basil.
Broil in the preheated oven until cheese has melted and is bubbling, about 1 minute, watching carefully so they don't burn.
