Cottage Cheese Omelet Muffins

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Cottage Cheese Egg Muffins are loaded up with eggs, veggies, and cottage cheese for a low-carb and protein-packed breakfast. Serve them right away or freeze them for later to enjoy the ultimate on-the-go healthy breakfast.

202 CAL 4g CARBS 11g FAT 20g PROTEIN 2

These Cottage Cheese Egg Muffins are the ultimate healthy low-carb breakfast. Whether you’re following keto or just looking for a high-protein breakfast, these delicious muffins do not disappoint. They are fluffy, flavorful, and beyond easy to make.

If you’re trying to add more protein to your diet but don’t always have the time to whip up an egg dish from scratch in the morning, this egg muffin recipe is your new best friend. It takes under 30 minutes to prepare from start to finish and freezes really well, meaning it’s the ideal healthy meal prep.

On more occasions than I can count, I have thanked my lucky stars that I had a few of these babies waiting patiently in the freezer. They’ve come in handy as easy breakfasts for my girls, on-the-go breakfasts for work, and tasty snacks when I needed an afternoon protein boost.

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. I have started adding cottage cheese to my scrambled eggs as well. Don't shy away from this just because you don’t like cottage cheese, I promise it's a whole different thing.

Not only are these Cottage Cheese Egg Muffins completely delicious, but they are also totally customizable. If you have no clue what to do with the leftover veggies in your fridge, just chop them up and toss them into your egg muffins. You can use any combination of veggies, meats, and cheeses to create the egg muffins of your dreams.

If you love egg muffins as much as I do, be sure to try out my Broccoli Cheddar Egg Muffins and Sweet Potato and Spinach Egg Muffins. With so many variations for delicious egg muffin recipes, you can enjoy a different one every day of the week!

Egg muffins with cottage cheese and vegetables cut in half and stacked on a plate.

Key Ingredients

To make these mouthwatering egg muffins, you will need the following key ingredients:

  • Eggs: What would an egg muffin be without eggs? The ultimate breakfast staple!
  • Cottage cheese: This protein-packed ingredient is the star of the show. It adds amazing flavor and a ton of protein in every bite. I prefer to use reduced-fat cottage cheese, but you can use any kind you like.
  • Veggies: This recipe calls for a combination of green bell peppers, onions, broccoli, and tomatoes. However, feel free to use any veggies you have at home.
  • Cheddar cheese: You can swap this out for another type of cheese like mozzarella, feta, parmesan, or goat cheese. Personally, I love the way cheddar cheese complements both the eggs and the veggies in this dish!

Recipe Tips and Tricks

Here are some of my top tips and tricks to help you make this dish:

  • The fat in the cheese helps keep the egg muffins from getting soggy, so I highly recommend using a full half cup!
  • If you’re making paleo egg muffins, try cooking the veggies ahead of time to cook out as much of the water as you can. This will help prevent the egg muffins from getting soggy.
  • To give your egg muffins a kick, feel free to add crushed red pepper or finely diced jalapenos to the recipe. You can also drizzle the baked egg muffins with sriracha just before serving for some delicious spicy flair and a pop of color.
  • I recommend using a silicone muffin tin for this recipe to prevent sticking. If you don’t have one, you can use paper liners to act as a barrier between the egg muffins and the metal tin. This will prevent you from losing the bottoms of your muffins to the tin!

Cottage Cheese Egg Muffin Variations

When it comes to egg muffins, the options for flavor combinations are endless. You can use any meats, cheeses, and veggies you like. Just keep in mind that you want around 1-1 ½ cups of toppings and 1 cup of cheese. Here are some of my favorite flavor combinations to try next:

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

Cottage cheese and egg muffins with vegetables served on a white plate.

How to Store Cottage Cheese Egg Muffins

Because they store so well, Cottage Cheese Egg Muffins make for the ultimate meal prep recipe! I always recommend making extra muffins to freeze for later. They’re perfect for the mornings when you wake up late or are too busy to make breakfast.

After pulling the egg muffins out of the oven, it’s important to let them cool down completely before transferring them to an airtight bag or container. Once you’ve secured them properly, you can store egg muffins in one of two ways:

  • In the fridge for up to 5 days.
  • In the freezer for up to 3 months.

Frequently Asked Questions

Below you will find the answers to some of the most frequently asked questions about this delicious dish:

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 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 them 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.

Absolutely. To reheat egg muffins, wrap them loosely in a paper towel and microwave them for 20 seconds if thawed or for 60 seconds if frozen. You can also reheat your egg muffins in the oven by baking them at 350°F for 10 minutes.

You can use any combination of vegetables, cheeses, herbs, spices, and meats to make egg muffins. It all depends on your dietary preferences, what you have at home, and what you’re in the mood for!

Of course! To make these egg muffins paleo-friendly, just leave out the cheese and add two extra eggs instead. You can also increase the amount of protein by adding meat like bacon or turkey to your egg muffins.

Baked cottage cheese, egg, and vegetable muffins with broccoli, red peppers, and cheddar cheese.
The Recipe
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Cottage Cheese Omelet Muffins

202 CAL 4g CARBS 11g FAT 20g PROTEIN 2
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  • 12 eggs
  • 1 cup reduced fat cottage cheese
  • 1/4 cup green peppers, chopped
  • 1/4 cup onion, chopped
  • 1/4 cup broccoli, chopped
  • 1 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.

Eggs being whisked with cottage cheese, vegetables cheddar cheese, salt, and pepper.

Pour the egg mixture into the muffin tin. Bake for 20-25 minutes until eggs are puffed up and cooked through. As the egg muffins cool, they will deflate slightly. This is normal.

Cottage cheese and egg mix being poured into a muffin tin.


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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
On Cottage Cheese Omelet Muffins
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April 13, 2024 - 17:29
These sound delicious. Going to try making them tomorrow. How full do you fill the cups in the muffin pan?
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May 29, 2023 - 10:36
Are these made in a 12 muffin pan?
Or 6? It says two muffins per serving.
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May 30, 2023 - 13:41
This recipe makes 12 standard-sized muffins! Most people find they need 2 muffins for a breakfast sied portion.
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May 20, 2023 - 05:08
How do I make 1, how much cottage cheese?
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September 19, 2023 - 10:48
If you are making just a single muffin, you would use about 1.5 tbsp of cottage cheese for one muffin.
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Megan Mack-Berger
July 1, 2022 - 08:34
Add a Rating:
These are absolutely scrumptious! I highly recommend them.
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April 13, 2022 - 08:32
Instead of making muffins out of this recipe, how do you think it would turn out if I cooked it like a frittata in a cast iron skillet? And would the cooking time/temperature need to be adjusted?
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March 29, 2022 - 08:19
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I just made these. They are awesome! I added red pepper, red onion, sharp cheddar cheese. I used frozen Broccoli florets, thawed and chopped in the food processor. My first pan I used the muffin papers and that did not work well. They stuck even though they were silicone papers. It worked better in the tin sprayed with Pam. Lots of Pam.
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Karen Draycott
August 14, 2018 - 08:16
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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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