Cottage Cheese Omelet Muffins

Cottage Cheese Omelet Muffins made with eggs, your favorite veggies, and cottage cheese are a protein packed, portable breakfast you will love. With just 100 calories and 10 grams of protein per muffin, these are a healthy make ahead breakfast you will make again and again. Jump to Recipe


These Cottage Cheese Muffins are packed with veggies and plenty of protein from the eggs and cottage cheese. Plus they are low carb and keto friendly. Love egg muffins? Check out these Broccoli Cheddar Egg Muffins and Sweet Potato and Spinach Egg Muffins.

Lately, I have been trying to add more protein to my breakfasts but I don't always have time to make a whole egg dish from scratch in the morning. That's where these delicious omelet muffins come in as the perfect on-the-go protein packed breakfast since you can make them ahead of time and then enjoy them all week. Plus it's easy to make a few different flavor combinations in one batch so you don't get bored.

Now let's talk about the cottage cheese for a minute. Adding cottage cheese to eggs is something I just started doing. Not only does it up the protein content, but it also creates this amazing texture and adds creaminess to the eggs. They become almost custard like and are delicious. I have even started adding cottage cheese to my scrambled eggs. Don't shy away from this just because you don' t like cottage cheese, I promise it's a whole different thing. My husband hates cottage cheese and he will happily eat these.

Once you have the base recipe down, you can add any veggies you like to make your own customized cottage cheese omelet muffins. Pretty much anything will work. You can also add things like bacon, sausage, deli meats, and your favorite cheese.

Omelet muffins with veggies on a cutting board with blurred kitchen background.

Can I freeze cottage cheese egg muffins?

Omelet muffins actually freeze really well. Make sure to let them cool completely first. Then place them on a plate or baking sheet in the freezer until for around 4 hours until they are frozen. Place in a freezer safe ziploc bag or container. If you don't want to freeze them individually on a plate, you can wrap them in plastic wrap and place directly in the ziploc bag. To reheat, place in the fridge overnight to defrost and then warm in the microwave in the morning. You can also reheat them directly from the freezer by microwaving them for 30-45 seconds or popping them in the toaster oven.

Is there a way to make Paleo omelet muffins?

Of course! Just leave out the cheese and replace the cottage cheese with 2 extra eggs. The texture will be a little bit different but they will still be really delicious. To kick up the protein count, you can add meat to the muffins. Ground beef or turkey work well as do Paleo friendly deli meats, bacon, or sausage.

Cottage Cheese Muffin Ideas

Looking for more flavor combinations for these yummy omelet muffins? Just keep in mind you want between 1-1.5 cups of toppings and around 1/2 cup of cheese. Here are some ideas to try:

  • Tomato, mozzarella, and basil
  • Ham, broccoli, and cheddar cheese
  • Bacon, zucchini, and mozzarella
  • Black beans, diced tomatoes, green onions, and cheddar
  • Diced turkey, roasted veggies, goat cheese
  • Peppers, onions, ham, and cheddar
  • Spinach, tomatoes, olives, and feta
  • Sausage, spinach, roasted red peppers, and mozzarella

Here are some tools that helped when I was preparing this recipe:

  • Muffin tin: Although I used a metal muffin tin for the photos, usually I reach for a silicone muffin tin for making egg muffins since they stick the least. It almost guarantees that your muffins will pop right out after cooking. If not, you may want to use paper liners for the muffins.
  • Cheese grater: Usually I prefer to grate my own cheese if I have time since I find the texture is better in recipes. Sometimes pre-grated cheese is coated with something extra to keep it from sticking together that can make the texture a little weird when it is cooked. Here is the box grater I use and I love that it has a little container to catch and measure whatever you are grating.
The Recipe
Cottage cheese muffins with mushrooms, tomatoes, and spinach on a wooden board.

Cottage Cheese Omelet Muffins

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  • 12 U eggs
  • 1 cup reduced fat cottage cheese
  • 1/4 cup green peppers, chopped
  • 1/4 cup onion, chopped
  • 1/4 cup broccoli, chopped
  • 1 U tomato, chopped
  • 1/2 cup reduced fat shredded cheddar cheese
  • Salt and pepper

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Preheat the oven to 350 degrees. Spray a muffin tin with cooking spray.


Whisk the eggs. Stir in the cottage cheese, vegetables, and cheddar cheese. Season with salt and pepper.


Pour the egg mixture into the muffin tin. Bake for 20-25 minutes until eggs are puffed up and cooked through.

Nutritional Facts
Serving Size: 2 muffins
Amount Per Serving
Calories 202
Calories from Fat 102
% Daily Value *
Total Fat 11g
Saturated Fat 4g
Monounsaturated Fat 0g
Polyunsaturated Fat 0g
Cholesterol 378mg
Sodium 336mg
Total Carbohydrate 4g
Dietary Fiber 1g
Sugars 3g
Protein 20g

* Percent Daily Values are based on a 2,000 calorie diet. Your daily values may be higher or lower depending on your calorie needs.

The Nutritional Values provided are estimates only and may vary based on the preparation method.

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About the author Meet Kristen McCaffrey
Hi, I’m the cookbook author, recipe developer, and food enthusiast behind Slender Kitchen. I am obsessed with making healthy food that is easy to prepare and absolutely delicious. Meal planning is my secret weapon and I hope I can make meal time easier for you with our tried and tested recipes and foolproof meal plans. Learn More
† We are a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for us to earn fees by linking to and affiliated sites.
On Cottage Cheese Omelet Muffins
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Karen Draycott
August 14, 2018 - 08:16
Add a Rating:
I made these and they were delicious! I made a big batch and froze some. Definitely will make again!
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January 28, 2019 - 14:58
So happy to hear you enjoyed them! The cottage cheese really does add something special.
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Liz Canada
June 30, 2018 - 08:03
Add a Rating:
Can't wait to try this Muffin omelet
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January 28, 2019 - 14:58
They are so yummy! Hope you enjoy them as much as we do.
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Maverick Beard ...
August 28, 2018 - 18:32
It's really a great and useful piece of info. I'm satisfied that you shared this useful information with us.
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christine lauri...
December 26, 2020 - 18:29
Are these regular size muffin pans?
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December 26, 2020 - 23:28
Yes. It's a standard muffin tin for the recipe.
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