Print

Did you make this? Snap a photo and tag us on Instagram at @thrivinghome so we can see your creations and cheer you on!

A baking rack with pepperoni pizza muffins and bowls of marinara sauce and grated Parmesan cheese.

High Protein Pepperoni Pizza Muffins

These soft, cheesy High Protein Pepperoni Pizza Muffins are made with 100% whole wheat and freeze beautifully. Perfect for quick lunches or snacks—just heat and dip in marinara!

Yield: 12 muffins 1x
Prep: 20 minutesCook: 18-22 minutesTotal: 0 hours
Units:
Scale:

Ingredients

  • 1 1/2 cups white or golden whole wheat flour (sub: 3/4 cup whole wheat + 3/4 cup all purpose)
  • 1/4 cup grated Parmesan cheese
  • 1 1/2 teaspoons baking powder
  • 2 teaspoons Italian seasoning, crushed in hand (sub: half dried oregano and half dried basil)
  • 1 teaspoon garlic powder
  • 1/2 teaspoon salt
  • 1 cup milk (I used 2%)
  • 1/2 cup cottage cheese (I used full fat Daisy brand; sub: 1/2 cup milk and pinch of salt)
  • 2 large eggs
  • 1 (12-ounce) jar or 1 1/2 cups pizza sauce (I used Raos brand; sub: marinara sauce)
  • 2 cups shredded mozzarella cheese
  • 1 1/4 cup (5 ounces) uncured pepperonis, finely chopped (I used Applegate turkey pepperonis)

Before You Begin! If you make this, please leave a review and rating letting us know how you liked this recipe! This helps our business thrive & continue providing free recipes.

Instructions

Make it Now:

  1. Prep: Preheat the oven to 375°F. Spray a 12-count muffin tin with oil and rub with a paper towel. Set aside.
  2. Dry Ingredients: In a large bowl, combine the flour, Parmesan cheese, baking powder, garlic powder, Italian seasoning, and salt.
  3. Wet Ingredients: In a blender, blend together the milk, cottage cheese, and eggs until smooth.
  4. Complete the Batter: Add the wet ingredients to the dry ingredients and stir just until combined (do not over mix). Fold in 1 1/2 cups of mozzarella cheese (reserve the rest for later) and 1 cup pepperoni (reserve the rest for later).
  5. Prep Muffins: Divide the batter evenly into the muffin tin (about 2 heaping tablespoons per muffin) and smooth the tops. Place a teaspoon of pizza sauce on the top of each muffin and gently swirl it into the top of the batter with a knife. Sprinkle the tops evenly with the reserved cheese and then the pepperoni. Press the pepperonis down a little bit (so they stay put).
  6. Bake: Bake on the middle rack for 18-22 minutes, or until a toothpick comes out clean. (Mine took 20 minutes in a Caraway non-stick metal pan.)
  7. Serve: Allow to cool slightly before running a knife around the edges popping the muffins out. Warm up the remaining pizza sauce and serve in ramekins for dipping along with the warm muffins.

To Freeze for Later: Place in a single layer in a freezer bag, squeeze out all the air, and seal tightly. Freeze flat at least until muffins are frozen solid.

To Prep From Frozen: Loosely wrap a muffin in a moist paper towel and microwave in 20-30 second increments until warmed through. (Mine took about 45 seconds.) Serve with warm pizza sauce for dipping.


Notes/Tips

  • What is white or golden wheat flour? A milder tasting and lighter colored whole wheat variety compared to traditional whole wheat flour. It retains all the nutritional benefits of whole wheat, including the bran, germ, and endosperm, making it a healthier alternative to refined flours. If you can’t find this variety, I’d suggest using half whole wheat and half all purpose flour. Look for King Arthur Golden Wheat or Wheat Montana Prairie Gold brands.
  • How to Send in a Lunch Box: Cut the muffin into fourths, warm in a moist paper towel in the microwave until hot, and place in a thermos. Include a small container of marinara/pizza sauce (seal tightly!) and fork for dipping.
© Author: Rachel Tiemeyer
Cuisine: American Method: Bake