Preheat and prep. Set the oven to 350°F (175°C). Line a 12-cup muffin tin with liners or lightly grease with cooking spray.
Whisk the wet ingredients. In a large bowl, whisk the eggs, Greek yogurt, olive oil, and pizza sauce until smooth. This creates a moist, flavorful base.
Combine the dry mix. In another bowl, stir together almond or oat flour, protein powder, baking powder, Italian seasoning, garlic powder, salt, and pepper.
Break up any clumps.
Bring it together. Add the dry mixture to the wet ingredients. Stir until just combined. The batter will be thick but scoopable.
Fold in the good stuff. Gently fold in mozzarella, Parmesan, pepperoni, chicken sausage (if using), bell pepper, red onion, and spinach.
Don’t overmix.
Fill the muffin cups. Divide the batter evenly among the 12 cups. If you like, add a tiny spoonful of extra pizza sauce on top and a pinch of cheese for a bakery-style look.
Bake. Place in the oven for 18–22 minutes. They’re done when the tops are set, lightly golden, and a toothpick comes out mostly clean with a few moist crumbs.
Cool briefly. Let the muffins rest in the pan for 5 minutes, then transfer to a rack.
This helps them firm up and prevents sogginess.
Serve. Enjoy warm with extra sauce for dipping. They’re also great at room temperature for lunchboxes.