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Kalyn's Kitchen

Pizza-Flavored Breakfast Muffins with Pepperoni

Pizza-Flavored Breakfast Muffins with Pepperoni are a fun idea for a “think outside the box” breakfast! These muffins have a lot of almond meal, cottage cheese, and Parmesan and just a tiny bit of whole wheat flour. Use Breakfast Recipes to find more ideas like this one.

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Pizza-Flavored Breakfast Muffins with Pepperoni, Mozzarella, Parmesan, and Oregano found on KalynsKitchen.com

I only order pizza for a very rare splurge, but when I do it’s a sure thing that I’ll be having cold pizza for breakfast the next morning.  I’m not sure whether it was that cold pizza breakfast memory, or my fondness for pepperoni in general, but recently I found myself thinking about creating some kind of breakfast muffin variation with the flavors of pizza.  It took me several failed attempts to get one I liked, but I’m very happy with these Pizza-Flavored Breakfast Muffins with Pepperoni that start with the basic idea behind Cottage Cheese and Egg Breakfast Muffins and add pieces of pepperoni, mozzarella string cheese sticks, and dried oregano for a pizza flavored breakfast.

These muffins are adapted from a recipe that uses a dough made of cottage cheese, white whole wheat flour, almond meal, Parmesan, egg, water, and baking soda, so this isn’t a gluten-free recipe.  I did find myself wondering how it would work if you just switched out the flour for more almond meal for a gluten-free version, so if anyone tries that variation I’d love to hear how it works. Or try my Low-Carb Egg Crust Breakfast Pizza if you want a low-carb breakfast with pizza flavors!

Pizza-Flavored Breakfast Muffins with Pepperoni, Mozzarella, Parmesan, and Oregano found on KalynsKitchen.com

Use a fine-mesh strainer to rinse the cottage and let it drain well. I cut the round pepperoni pieces into sixths and sliced the mozzarella sticks into thin slices, then chopped a few of the cheese slices a bit more. Stir together the drained cottage cheese, Parmesan cheese, white whole wheat flour, almond meal (not finely ground almond flour), baking powder, salt, dried oregano, and Spike Seasoning. Mix the beaten eggs and water into the batter mixture.

Pizza-Flavored Breakfast Muffins with Pepperoni, Mozzarella, Parmesan, and Oregano found on KalynsKitchen.com

Then gently fold in the chopped pepperoni and sliced mozzarella string cheese sticks. Scoop the batter into muffins cups that have been sprayed with nonstick spray or olive oil. Bake at 400F/200C oven until the muffins are lightly browned and firm, about 30-35 minutes. The result is an eggy muffin with a coarse texture from the almond meal, with chunks of pepperoni and mozzarella cheese and a nice pizza-like flavor; enjoy!

More Breakfasts with Pizza Flavors:

Pepperoni Pizza Keto Crustless Quiche from Kalyn’s Kitchen
Breakfast Casserole with Sweet Italian Sausage, Mushrooms, and Cheese from Kalyn’s Kitchen
Breakfast Pizza from The Kitchn
Low-Carb Egg Crust Breakfast Pizza from Kalyn’s Kitchen

Weekend Food Prep:

This recipe has been added to a new category called Weekend Food Prep to help you find recipes you can prep or cook on the weekend and eat during the week!

Pizza-Flavored Breakfast Muffins with Pepperoni

For a “think outside the box” breakfast, these Pizza-Flavored Breakfast Muffins with Pepperoni are a fun idea!


  • 1/2 cup cottage cheese, rinsed and drained well (low-carb or full-fat cottage cheese will both work)
  • 1/3 cup finely grated Parmesan cheese
  • 1/4 cup white whole wheat flour
  • 2/3 cup almond meal or almond flour
  • 1 tsp. baking powder
  • 1/4 tsp. salt
  • 1 tsp. dried oregano (I used Greek oregano)
  • 1 tsp. Spike Seasoning (optional, or use any all-purpose seasoning that you like with eggs)
  • 4 eggs, beaten
  • 3 T water
  • 1/2 cup diced pepperoni, either turkey or pork pepperoni will work (I cut the pepperoni rounds into sixths)
  • 4 string cheese mozzarella sticks, cut into slices and some slices cut into smaller pieces (3/4 cup chopped mozzarella pieces)


  1. Put cottage cheese into a fine-mesh strainer and rinse with cold water, then let drain while you prep other ingredients.
  2. Preheat oven or toaster oven to 400C/200F.
  3. Spray silicone muffin cups or muffin pan with nonstick spray or olive oil.
  4. While cottage cheese drains, chop the pepperoni.  (I cut the round pepper pieces into sixths to make pie-shaped pieces, but you could cut them smaller if you prefer.)
  5. Slice the string cheese mozzarella sticks, then chop some of the slices to make various-sized pieces of cheese.  (You could probably use 3/4 cup grated mozzarella, but I liked the chunks of cheese in this.)
  6. When the cottage cheese has drained, mix together cottage cheese, Parmesan, flour, almond meal, baking powder, salt, dried oregano, and Spike Seasoning.
  7. Beat eggs with a fork, then beat in 3 tablespoons water.
  8. Add the egg mixture to the other ingredients and stir until combined.
  9. Add the chopped pepperoni and sliced string cheese to the batter and gently stir to combine.
  10.  Spoon the mixture into the sprayed baking cups of muffin tin, dividing evenly between the cups.
  11.  Bake 30-35 minutes, or until the muffins are lightly browned and set.
  12.  Eat while warm.
  13.  You can let these cool and store for several days in the refrigerator in a plastic container with a snap-tight lid.  Reheat the muffins in the microwave just until barely warm (about 1 minute,   depending on your microwave.)


Recipe inspired by Cottage Cheese and Egg Breakfast Muffins, which were adapted from Cottage Cheese Muffins at 101 Cookbooks, adapted from a recipe by Rose Elliot.)

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Low-Carb Diet / Low-Glycemic Diet / South Beach Diet Suggestions:
Pizza-Flavored Breakfast Muffins with Pepperoni do have a lot of low-carb and low-glycemic ingredients, but the small amount of flour probably makes this not suitable if you’re really limiting carbs. The muffins would be phase 2 or 3 for the South Beach Diet, due to the use of flour, and it would be important to use low-fat cottage cheese, lower-fat turkey pepperoni, and low-fat string cheese mozzarella sticks if you’re making this for South Beach. Even with those ingredients, this is a calorie dense muffin due to the fat content, since Parmesan and almond meal both add fat, so use portion control and don’t have nuts for a snack on a day you eat these if you’re following South Beach.

Find More Recipes Like This One:
Use the Diet Type Index to find recipes suitable for a specific eating plan. You can also Follow Kalyn’s Kitchen on Pinterest to see all the good recipes I’m sharing there.

Nutritional Information?
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    22 Comments on “Pizza-Flavored Breakfast Muffins with Pepperoni”

  1. Any suggestions on what to use in these for a low carb diet instead of cottage cheese or ricotta cheese. I can't disguise either one and I have a picky eater when it comes to some things. Thanks!