Cottage Cheese Pizza Muffins
Cottage Cheese Pizza Muffins are the easy, savory snack your family will love. These simple muffins stir together in minutes. They’re perfect for kids’ lunch boxes or a quick after-school bite. Protein-rich cottage cheese and other wholesome ingredients make them more nutritious than typical muffins. You still get all the cozy, pizza-inspired flavors kids crave. A fun, freezer-friendly recipe you’ll want to make again and again!

Kids in the Kitchen:
- Very simple task: have kids place the paper muffin liners into the muffin tin. No mess at all!
- Practice egg cracking: Kids can crack the eggs into the bowl before adding anything else, so you can easily remove any shells.
- Measure and mix the dry ingredients: depending on the age or your child and/or how much time you have to bake, you may want to measure many of the ingredients before inviting your child to bake with you. You can leave a couple things for your child to measure, such as the baking powder and salt.
- Topping: If kids only do one little thing to help with the recipe, let it be this: have them add a pinch of cheese and a few pieces of pepperoni, if using, to the top of each muffin. So easy and fun!
Subs and Tips for Making Cottage Cheese Pizza Muffins:
- Flour: I like to use a mix of all-purpose and whole wheat flours for this recipe. However, you can use all of either of those if you prefer. Whole wheat tends to absorb more liquid than all-purpose, so if you are using all whole flour, use a total of 1 3/4 cups.
- Gluten-free: A gluten-free cup-for-cup style flour will work will in this recipe to make it gluten-free.
- Egg-free: You can omit the egg in the recipe and replace it with 3 tablespoons of milk.
- Cottage cheese: a small-curd style cottage cheese works best in this recipe. However, if you use a cottage cheese with larger curds, you can just squish them a little with a fork so you don’t see big pieces in the finished muffins.
- Vegetarian: you can omit the pepperoni to make the muffin vegetarian.
- Veggies: I like to add a little chopped spinach to the muffins. However, you can totally leave that out or mix in some grated carrot or finely chopped bell pepper if you prefer.
- Helpful tools: Unbleached parchment paper liners, large cookie scoop (in picture below), and my favorite muffin tin are listed in my Baking Essentials list on Amazon HERE.


Cottage Cheese Pizza Muffins
High protein, savory muffins great for lunch boxes and snacks.
Ingredients
- 1 cup all-purpose flour
- 1 cup whole wheat flour or another cup of all-purpose, See note for flour subs
- 1 tsp baking powder
- 1/2 tsp baking soda
- 1/4 tsp salt
- 1/2 tsp dried Italian seasoning or dried oregano, optional
- 1 cup cottage cheese, preferably small-curd style I use low-fat
- 1 large egg or 3T extra milk
- 1/4 cup avocado or vegetable oil
- 1/3 cup jarred marinara sauce
- 1 cup milk (any kind)
- 1 cup shredded mozzarella cheese, divided
- 1 cup baby spinach, finely chopped, optional
- 1/2 cup mini pepperoni or large pepperoni, chopped (optional)
Instructions
- Heat the oven to 400 degrees. Place paper liners in a muffin tin or grease with oil spray.
- To a medium bowl, add the flour, baking powder, baking soda, salt, and dried herbs, if using. Whisk to combine.
- In a large bowl, whisk together the cottage cheese, egg, oil, marinara sauce, and milk.
- Add the flour mixture to the bowl and use a large spoon or rubber spatula to mix. Before the the flour is fully mixed in, add the 3/4 cup mozzarella, spinach, and 1/2 of the pepperoni, if using. Continue to mix until everything is just incorporated.
- Divide the batter between the muffin cups, filling mostly to the top. Sprinkle a pinch of cheese over each muffin then add a few pieces of pepperoni, if using.
- Bake until golden brown on top and cooked through, 12 to 14 minutes.
- Once muffins are cool, store in an airtight container at room temp for 1 day or in the refrigerator for 4 to 5 days. The muffins can also be well wrapped and frozen for 1 month.
Notes
To use all whole wheat flour in this recipe, use 1 3/4 cups total.
To use gluten-free flour, use 2 cups total.
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Other Recipes to Try:
Cottage Cheese Blueberry Muffins
Blender Cottage Cheese Pancakes
High Protein Tortilla Egg Cups