Pizza Muffins

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Let’s mix things up with some delicious little Pizza Muffins!  Think of these savory pizza muffins as the cool cousin of the muffin family. We’re ditching the sweet stuff and going full-on savory with freshly milled flour, which tastes amazing and gives you a nice nutritional boost. Whether you’re looking for a quick snack, an easy dinner, or something to pack in lunch boxes, these whole wheat muffins will become a favorite the whole family will love, pleasing even those picky eaters. Plus, it’s super fun to make bite-sized snacks!

Are you looking for more Freshly Milled Flour recipes? Check out our amazing Whole Wheat Bread, our easy Whole Wheat Pancakes , or our amazing moist Banana Cake with Cream Cheese Frosting. And don’t forget to download our FREE Wheat Berries infographic  HERE.


Using freshly milled flour in your baking is like hitting the nutrient jackpot. Here’s the thing: in commercial flour production, grains are milled and then sit for a while before reaching your kitchen. This process, especially when it involves refining, strips away the bran and germ — the parts of the grain richest in nutrients like fiber, vitamins, and minerals. What you’re left with is mostly just the starchy endosperm.

But when you mill flour at home, you keep all those good bits intact. The bran, for instance, is a powerhouse of fiber, which aids in digestion and keeps you feeling full longer. The germ is packed with essential nutrients like vitamin E, zinc, and magnesium. So, by milling your flour and using it immediately, you’re ensuring that none of that goodness is lost to time and processing.

This means that your savory muffins aren’t just tasty; they’re also a healthier option. They bring more to the table in terms of nutrition, providing a more complete range of the grain’s natural benefits. Plus, freshly milled flour can also give your baked goods a richer flavor and better texture, making your muffins not just nutritious, but also irresistibly delicious. So, you’re not only feeding your body better but also treating your taste buds to a more flavorful experience. Can you see why I’m so passionate about freshly ground flour?

What you’ll love about this Easy Pizza Muffins Recipe:

  • Quick and Easy: These pizza muffins are a breeze to make. You can get them in the oven fast, making them perfect for a last-minute meal or after school snack.
  • Mix it Up: Throw in your favorite pizza toppings! It’s all about making them your way, whether it’s with loads of cheese, veggies, or meats.
  • Tasty and Healthy: With freshly milled flour, they’re not just yummy but also good for you. It’s like having your pizza but in the form of a muffin with a wholesome twist.

Recipe Ingredients

You’ll need the following ingredients to make these amazing Easy Pepperoni Muffins:


  • Freshly Milled Flour: 
  • Baking powder
  • Salt and garlic powder
  • Italian seasoning for that classic pizza flavor
  • Milk, eggs, and avocado oil
  • Shredded mozzarella and Parmesan cheese for cheesy goodness
  • Sun-dried tomatoes- If you don’t like these, simply leave out!
  • Chopped pepperoni, (or use mini pepperonis) or use any other favorite toppings


Check out the quick visual guides below. For full instructions and ingredients, see the printable recipe card at the end.

  1. Preheat the oven to 400°F and get your muffin pan ready, either greased or lined with muffin cups.
  2. In a large bowl, whisk together the dry ingredients, adding a pinch of Italian seasoning for that authentic pizza taste.
  3. In a separate bowl, mix the wet ingredients, then combine them with the dry ones, being careful not to overmix.
  4. Fold in the mozzarella cheese, Parmesan, and chopped toppings until the mixture is just right.
  5. Scoop the mixture into the muffin cups, filling them about two-thirds full, and bake until they turn golden brown, about 18-20 minutes.
  6. Let them cool in the pan before transferring to a wire rack;  serve them warm with a side of pizza sauce or marinara for dipping.

Pro Tip:

The #1 tip for making these easy pepperoni pizza muffins is to not overmix the batter. Mixing just until the ingredients are combined helps keep the muffins light and fluffy, ensuring they have the perfect texture once baked.

Storage and Reheating

Storage: Store leftovers on the counter in an airtight container for up to 2 days. For longer storage, place them in an airtight container in the refrigerator. They will keep well for up to 1 week.

To Reheat: Place a muffin on a microwave-safe plate and heat for about 30 seconds to 1 minute, or until it’s warmed throughout. Be careful not to overheat, as this can make the muffins tough.

To Freeze: Wrap each muffin tightly in plastic wrap or aluminum foil. This helps prevent freezer burn and makes it easy to grab one at a time. Place the wrapped muffins in an airtight container or a freezer Ziploc bag to protect them from absorbing flavors from the freezer. Store in the freezer for up to 3 months. Thaw the muffins in the refrigerator overnight or leave them at room temperature for a few hours. Once thawed microwave as mentioned above. If reheating directly from frozen, you might need to add a few extra minutes to the reheating time in the oven to ensure they are warmed throughout.

Additions & Substitutions


  • Veggies: Add in diced onions, mushrooms, or spinach for an extra nutrient boost and flavor.
  • Meats: Besides pepperoni, consider adding cooked Italian sausage, bacon bits, or chicken pieces.
  • Cheese Variety: Mix in some cheddar, feta, or goat cheese for a different taste.
  • Herbs and Spices: Fresh basil, oregano, or a sprinkle of red pepper flakes can enhance the flavor. I keep it mild for my kids, but you can add your favorite things. I personally enjoy adding black olives to mine!


  • Freshly Milled Soft White Flour: I’ve made this recipe with hard white wheat and soft white wheat. Both works, but I find the soft white wheat yields a more delicate crumb and therefore more crumbly. I usually stick with the hard white for this recipe. 

FAQs about about this Pepperoni Pizza Muffins Recipe:

Yes, you can prepare these muffins ahead of time and store them in the refrigerator or freezer until you’re ready to serve. They reheat well, making them a convenient make-ahead meal or snack.

While muffin liners usually prevent sticking, lightly greasing the top of the muffin pan can help ensure the muffin tops don’t stick to the pan if they overflow a bit.

The muffins are done when they are golden brown on top and a toothpick inserted into the center of a muffin comes out clean or with a few moist crumbs attached.

What Can I Serve with this Easy Pepperoni Pizza Muffins Recipe?

Pair these pepperoni muffins with a big salad, or with Pasta e Fagioli Soup for a heartier meal.

I always serve extra pizza sauce or marinara sauce on the side. These tasty little pizza bites are great for pizza night, game day, or as extra snacks for those busy days!

Pizza muffins on stacked plates with a side of pizza sauce in a little white dish.

Pizza Muffins
These pizza muffins are a yummy twist on the classic pizza, baked into portable, bite-sized treats. Made with freshly milled flour, they’re packed with savory flavors from melted mozzarella, Parmesan, and a medley of your favorite pizza toppings like pepperoni and sun-dried tomatoes.
5 from 1 vote
Prep Time 10 minutes
Cook Time 18 minutes
Total Time 28 minutes
Course Lunch
Cuisine American
Servings 12 muffins
Calories 148 kcal


  • 2 cups freshly milled hard white flour
  • 1 tablespoon baking powder
  • 1/2 teaspoon salt
  • 1/2 teaspoon garlic powder
  • 1 teaspoon Italian seasoning
  • 1 cup milk
  • 1/3 cup avocado oil
  • 2 large eggs
  • 1 cup shredded mozzarella cheese
  • 1/2 cup grated Parmesan cheese
  • 1/2 cup pepperoni slices chopped
  • 1/2 cup sun-dried tomatoes chopped


  • Preheat the oven to 400°F. Grease a 12-cup muffin pan or line it with paper liners.
  • In a large bowl, whisk together the freshly milled whole wheat flour, baking powder, salt, garlic powder, and Italian seasoning.
  • In a separate bowl, combine the milk, oil, and eggs. Whisk until well blended.
  • Add the wet ingredients to the dry ingredients and stir until just combined. Do not overmix.
  • Fold in the mozzarella cheese, Parmesan cheese, chopped pepperoni, and sun-dried tomatoes.
  • Divide the batter evenly among the prepared muffin cups, filling each about 2/3 full.
  • Bake for 18-20 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
  • Remove the muffins from the oven and let them cool in the tin for 5 minutes before transferring them to a wire rack to cool completely.
  • Serve warm with marinara sauce for dipping.


The #1 tip for making these easy pepperoni pizza muffins is to not overmix the batter. Mixing just until the ingredients are combined helps keep the muffins light and fluffy, ensuring they have the perfect texture once baked.


Calories: 148kcalCarbohydrates: 5gProtein: 6gFat: 12gSaturated Fat: 4gPolyunsaturated Fat: 1gMonounsaturated Fat: 6gTrans Fat: 0.1gCholesterol: 18mgSodium: 421mgPotassium: 219mgFiber: 1gSugar: 3gVitamin A: 175IUVitamin C: 2mgCalcium: 176mgIron: 1mg
Keyword 30 minute meals, Dinner, freshly milled flour, kid approved, pizza, snacks
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