Preheat and prep the pan. Set your oven to 350°F (175°C).
Line a 12-cup muffin tin with silicone liners or lightly grease each cup with olive oil. Silicone liners help prevent sticking and make cleanup easier.
Combine dry ingredients. In a large bowl, whisk 1 1/2 cups almond flour, 1/3 cup unflavored whey protein isolate, 2 teaspoons baking powder, 1/2 teaspoon sea salt, 1 teaspoon Italian seasoning, 1/2 teaspoon garlic powder, and 1/2 teaspoon onion powder. Break up any clumps for an even batter.
Mix the wet ingredients. In a separate bowl, whisk 3 large eggs, 1/2 cup full-fat Greek yogurt, and 2 tablespoons olive oil until smooth.
The yogurt keeps the muffins tender and boosts protein.
Bring it together. Pour the wet mixture into the dry bowl. Stir just until combined—don’t overmix. Fold in 1 cup shredded mozzarella, 1/4 cup grated Parmesan, and 1/2 cup mini pepperoni.
If using extra mix-ins, add up to 3/4 cup total so the batter stays sturdy.
Portion the batter. Divide the batter evenly among the 12 muffin cups. Each cup should be about three-quarters full. For a pizza look, press a few extra pepperoni pieces on top and sprinkle with a little mozzarella.
Bake. Bake for 16–20 minutes, until the tops are golden and a toothpick inserted in the center comes out clean.
If the tops brown too quickly, tent loosely with foil for the last few minutes.
Cool before removing. Let the muffins cool in the pan for 5–10 minutes. This helps them set and release cleanly. Transfer to a wire rack to finish cooling.
Serve. Enjoy warm with a side of warm, low-sugar marinara for dipping.
Garnish with a sprinkle of Parmesan or red pepper flakes for a little kick.