High Protein Pepperoni Pizza Muffins
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These High Protein Pepperoni Pizza Muffins make the perfect grab-and-go lunch or snack. Each serving has 26 grams of protein and is made with 100% whole wheat. They’re soft, cheesy, and taste like mini calzones. Best of all? They freeze and reheat beautifully. Just warm one up and dip it in pizza sauce!
Why We Love This Recipe
I’m really pumped about this fun recipe that I crafted, tweaked, and perfected over several tests. Kids and adults love these Pizza Muffins, and my family declared that they taste like pepperoni calzones!
Here’s what’s to love:
- High in protein–packed with over 25 grams protein per serving!
- 100% whole wheat
- Cheesy, soft texture–even after freezing and rewarming!
- Freezer-friendly. Warm them straight from the freezer for quick lunches or snacks.
- Delicious dipped in Pizza Sauce or served with Tomato Bisque for dipping.
Ingredients
Open your pantry and fridge to find most of these simple, wholesome ingredients.
Ingredient Notes
- White or golden whole wheat flour – The secret to making these a light whole wheat savory muffin is using using white whole wheat flour, like Prairie Gold, versus the traditional whole wheat made from red wheat. Important: If you can’t find that specific kind of flour, use half whole wheat and half unbleached, all-purpose flour instead.
- Baking powder – Make sure your baking powder isn’t expired. If it is, test to see if it’s still working by adding a little bit to a bowl with some vinegar. If there is a reaction, it’s still good.
- Cottage cheese – A lot of the protein comes from this ingredient. I used 4% fat Daisy brand because of the clean ingredients.
- Pizza Sauce – You can make our homemade version or, you can use your favorite marinara sauce. I like Raos brand
- Uncured pepperonis – Check the ingredients of the ones you buy. I used Applegate turkey pepperonis because they have the best ingredients and they taste great.
How to Make Pepperoni Pizza Muffins
Here’s a quick overview of how to make these Pepperoni Pizza Muffins. However, a full, printable recipe is at the bottom of this blog post.
Prep
Preheat the oven to 375°F. Spray a 12-count muffin tin with oil and rub with a paper towel. Set aside.
Dry Ingredients
In a large bowl, combine the flour, Parmesan cheese, baking powder, garlic powder, Italian seasoning, and salt.
Wet Ingredients
In a blender, blend together the milk, cottage cheese, and eggs until smooth.
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).
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).
Bake & Serve
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.)
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.
Can I Freeze Pizza 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.
Recipe FAQs
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.
Here’s the method I came up with for my kids, and they said it stayed warm until lunch and was really yummy…
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.
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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!
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)
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Instructions
Make it Now:
- Prep: Preheat the oven to 375°F. Spray a 12-count muffin tin with oil and rub with a paper towel. Set aside.
- Dry Ingredients: In a large bowl, combine the flour, Parmesan cheese, baking powder, garlic powder, Italian seasoning, and salt.
- Wet Ingredients: In a blender, blend together the milk, cottage cheese, and eggs until smooth.
- 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).
- 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).
- 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.)
- 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.
This is the perfect recipe I was looking for. Sounds amazing. Do you think an all purpose GF flour would make a good substitute for whole wheat?
I haven’t tested it with GF flour yet, but I usually have good luck with Bob’s Red Mill 1:1 gluten free flour. Please let me know how they turn out if you try it!
I used King Arthur GF Measure for Measure Flour and it worked great! I think next time I will increase the time a few more minutes (did 20 mins) but my kids loved these. Pizza Night reinvented..thanks!
Thank you so much for this feedback on the GF sub. That’s really great to know. Appreciate it!