Preheat oven to 325°F/160°C. Grease mini muffin pan, or use liners.
In a large bowl, whisk together almond flour, whey protein, Italian seasoning, baking powder, garlic powder, and salt. Add cheese and pepperoni; stir to combine.
Stir in eggs, butter, and almond milk until combined. Fill muffin cups about 3/4 full.
Bake for 17-20 minutes, until golden brown and slightly firm to the touch. Let cool in pan for 10 minutes, then transfer to cooling rack. Serve with low carb pizza sauce or marinara.