Preheat your oven to 375°F (190°C) and grease a muffin tin with cooking spray or butter.
In a large mixing bowl, whisk together the flour, baking powder, garlic powder, Italian seasoning, and salt until well combined.
Stir in the shredded mozzarella cheese and diced pepperoni until evenly distributed.
In a separate bowl, whisk together the milk, egg, and melted butter until smooth.
Pour the wet ingredients into the dry ingredients and mix until just combined. Do not overmix.
Spoon the batter into the prepared muffin tin, filling each cup about ¾ full.
Bake in the preheated oven for 18-20 minutes, or until the tops are golden brown and a toothpick inserted into the center comes out clean.
Allow the pizza cupcakes to cool in the pan for 5 minutes before transferring them to a wire rack. Serve warm with marinara sauce for dipping.