Preheat your oven to 375°F (190°C). Grease a muffin pan or line it with paper liners.
In a large mixing bowl, combine the whole wheat flour, baking powder, baking soda, salt, dried oregano, dried basil, garlic powder, and onion powder.
In another bowl, whisk together the eggs, olive oil, and whole milk. Stir in the pizza sauce until well combined.
Pour the wet ingredients into the bowl with the dry ingredients and mix until just combined.
Fold in 1/2 cup shredded mozzarella cheese and 1/4 cup grated Parmesan cheese. Optional: Add mix-ins into the batter, like chopped pepperoni or cooked sausage.
Spoon the batter into the prepared muffin pan, filling each cup about 3/4 full.
Sprinkle a little shredded mozzarella cheese on top of each muffin.
Add your desired toppings on top of each muffin, such as pepperoni, black olives, sausage, or bell peppers.
Bake for 18-20 minutes, or until the muffins are golden brown and a toothpick inserted into the center comes out clean.
Allow the muffins to cool in the pan for a few minutes before transferring them to a wire rack to cool completely.
Serve with extra pizza sauce for dipping. Enjoy!