Kalyn's Kitchen

Cottage Cheese Breakfast Muffins with Bacon

Cottage Cheese Breakfast Muffins with Bacon also have egg, Parmesan, almond flour, and white whole wheat flour for a tasty low-carb muffin. See suggestions to replace the flour for a version that’s Keto and gluten-free.

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Cottage Cheese Breakfast Muffins with Bacon finished muffins on plate

When I spotted the idea for cottage cheese egg muffins online I loved the idea of a high-protein muffin with cottage cheese, eggs, Parmesan, and almond meal, with just the tiniest bit of flour, and I decided to make them as a breakfast muffin. And I have to say these Cottage Cheese Breakfast Muffins with Bacon were definitely a success! Since I first posted this recipe I have made these delicious breakfast muffins over and over to keep in the fridge for a grab-and-go breakfast.

These muffins have just the tiniest bit of flour, so they’re still a very low-carb breakfast choice, but the use of a little flour plus ingredients like cottage cheese, almond flour, and Parmesan cheese make them very different in flavor and texture than my popular Low-Carb and Keto Egg Muffins. If you don’t want flour or want a muffin that’s Keto or Gluten-Free, keep reading for suggestions for that! 

What ingredients do you need for this recipe?

  • cottage cheese
  • grated Parmesan cheese
  • White Whole Wheat Flour (affiliate link), or see Keto and Gluten-Free options below
  • Almond Flour (affiliate link)
  • baking powder
  • salt
  • water
  • eggs
  • bacon
  • green onion

What if you need a breakfast muffin that’s gluten-free or Keto?

If you check the nutritional information you’ll see that the small amount of white whole wheat flour doesn’t add many carbs, and the flour does give a nice texture to the egg muffins with cottage cheese. But if you need a version that’s gluten-free or Keto or you just don’t want to use flour I’d recommend replacing the flour with Flaxseed Meal (affiliate link) or Hemp Seeds (affiliate link), or maybe a combination of both those. There’s also a delicious gluten-free breakfast muffin on the blog that was partly inspired by this recipe.

Want more ideas for breakfast muffins like this?

I love these cottage cheese and egg muffins so much that I’ve made a variation with ham and cheddar and a meatless version with mushrooms and Feta! Try the recipe yourself and see if these are going to become a repeater for you too! And you can check out my post with Low-Carb Muffins and Breakfast Muffins for lots more tasty muffin idea!

Cottage Cheese and Egg Breakfast Muffins with Bacon photo collage

How to Make Cottage Cheese Breakfast Muffins with Bacon:

(Scroll down for complete printable recipe, including nutritional information.)

  1. Preheat oven to 400F/200C.
  2. Spray silicone baking cups (affiliate link) lightly with olive oil or non-stick spray. 
  3. Mix together the cottage cheese, Parmesan, white whole wheat flour, almond meal, salt, water, and beaten egg.
  4. Then fold in the crumbled pre-cooked bacon and thinly sliced green onion.
  5. Fill large muffin cups 3/4 full.
  6. Bake 25-30 minutes, or until muffins are light browned and enjoy! 
  7. One of these muffins is enough for me for a tasty breakfast!

Cottage Cheese and Egg Breakfast Muffins Recipe with Bacon and Green Onions found on KalynsKitchen.com.

More High Protein Muffin Recipes:

Low-Carb and Keto Egg Muffins
Flourless Savory Breakfast Muffins
Green Chile and Cheese Egg Muffins

Weekend Food Prep:

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

Cottage Cheese  Breakfast Muffins with Bacon

Cottage Cheese Breakfast Muffins with Bacon

Yield 6 muffins
Prep Time 20 minutes
Cook Time 30 minutes
Total Time 50 minutes

Cottage Cheese Breakfast Muffins with Bacon have cottage cheese, egg, almond flour, and and just a little white whole wheat flour for a tasty breakfast muffin! See suggestions in the recipe if you need a version that's gluten-free.


  • 2/3 cup cottage cheese (see notes)
  • 1/2 cup grated Parmesan cheese
  • 1/4 cup white whole wheat flour (see notes for gluten-free option)
  • 2/3 cup almond flour
  • 1 tsp. baking powder
  • 1/2 tsp. salt
  • 3 T water
  • 4 eggs, beaten
  • 3 strips cooked bacon
  • 3 T thinly sliced green onion


  1. Preheat oven to 400F/200C. Spray silicone baking cups (affiliate link) lightly with olive oil or non-stick spray.
  2. In mixing bowl, combine cottage cheese, Parmesan cheese, white whole wheat flour, Almond Flour (affiliate link), salt, water, and beaten egg. Mix well.
  3. Gently mix in crumbled bacon and green onion, until well distributed in batter.
  4. Fill muffin cups 3/4 full with cottage cheese and egg mixture.
  5. Bake 25 -30 minutes, until muffins are firm and lightly browned.
  6. Serve hot or room temperature.


To make a version that's gluten-free I would replace the white whole wheat flour with Flaxseed Meal (affiliate link) or Hemp Seeds (affiliate link), or use a combination of both. Some people have also reported using quinoa flakes.

Use regular or low-fat cottage cheese, whichever you prefer.

Muffins can be refrigerated and reheated in the microwave. (I cut in half crosswise before heating. Be very careful not to microwave too long, or they will become tough.) I haven’t tried freezing them, but I would imagine they will freeze well.

Recipe adapted from Sundried Tomato Cottage Cheese Muffins by Rose Elliot, featured on 101 Cookbooks.

Nutrition Information:



Serving Size:


Amount Per Serving: Calories: 224Total Fat: 15gSaturated Fat: 4gUnsaturated Fat: 10gCholesterol: 141mgSodium: 659mgCarbohydrates: 9gFiber: 2gSugar: 1gProtein: 15g

Nutrition information is automatically calculated by the Recipe Plug-In I am using. I am not a nutritionist and cannot guarantee 100% accuracy, since many variables affect those calculations.

If you make this recipe I'd love to hear how it turns out. Leave a star rating or share on social media with the hashtag #KALYNSKITCHEN, thanks!

Cottage Cheese and Egg Breakfast Muffins with Bacon thumbnail photo

Low-Carb Diet / Low-Glycemic Diet / South Beach Diet Suggestions:
These Cottage Cheese Breakfast Muffins with Bacon are quite low in net carbs, even with the small amount of white whole wheat flour. See suggestions in the recipe for Keto and Gluten-Free options to replace the flour if you prefer. These muffins would be phase 2 or 3 for the original South Beach Diet due to the flour. I wouldn’t worry about the small amount of bacon here for South Beach, but use turkey bacon if you prefer. The almond meal makes these muffins relatively high in fat, so be aware of your other food choices that day if you’re following South Beach.

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

Historical Notes for this recipe
Cottage Cheese Breakfast Muffins with Bacon were first posted October 2007 and updated with better photos, September 2015. The recipe was last updated with more information in September 2021.

Pinterest image of Cottage Cheese Breakfast Muffins with Bacon

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    47 Comments on “Cottage Cheese Breakfast Muffins with Bacon”

  1. I've never had anything like it. Looks great

  2. I made these last week using soy flour. They were delicious both warm and cold, I really didn't bother warming them up the following 2 days. I had 14 of them, made in smaller silicon moulds.

  3. I also would like to know what to use in place of Almond flour, almonds etc. The specialty flours and such are really expensive for small bags where I live. I have oats, chia, couscous, and things like that as well as other (regular) flours. Thank you!!

    • Linda, I haven't made them with anything but almond flour and I'm afraid I'm not a good enough baker to know what else might substitute. One commenter has recommended soy flour, but I haven’t done that myself. If you make them sucessfully with something else, I'd love to know about it.

  4. Mmmmmm I really want to make those tonight! I have no almond meal, what can I substitute them for? Oat flour, more whole wheat flour? Those are the stuff I have around…

    • I'm afraid I can't offer any suggestions about what to substitute for almond meal; I”m not that good of a baker. One commenter has recommended soy flour, but I haven’t done that myself. If you make them sucessfully with something else, I'd love to know about it.

  5. These look so great – hearty enough to fill you up, but still really healthy. I need to use cottage cheese more often, it's not something I ever really buy.

  6. If you use the silicone baking cups (I now prefer the individual ones) that will keep them from sticking. I don't think paper would work for this, even with flour (and personally I would not use flour; that defeats the purpose of a relatively low-carb breakfast like this.) Even a well-sprayed metal muffin pan would be better than paper muffin liners.

  7. Great taste, but even with the well oiled muffin cups, they still terribly stuck and when paper cup was pealed off, a 1/4 of the muffin went with to :(. I wonder if flour or maybe even corn flour would prevent it from sticking?

  8. Cyndi I would guess it might be partly because I'm at high altitude? And those silicone muffin pans I used in the photo are a bit on the large side. Glad you enjoyed them.

  9. I made these for the first time today; followed the directions exactly except for the oven temperature (mine runs hot), which I set at 350˚. Two big differences from yours: The recipe filled up 12 regular-sized muffin tins, and they came out almost over-done after 25 minutes. I'm thinking that's because of the oven temp – I need to do a temperature test. But I'm wondering why it made so many. Verdict: wonderful. I used a little salsa and am nice and full.

  10. I've been experimenting with hemp hearts, and I'm going to try those in these muffins to replace the flour!

  11. I used to follow the recipe as written, with the exception of the flour, I used soy flour instead. But this time I was looking to lighten it up, so I eliminated the egg yolks and just used the whites instead, along with the soy flour. I also had to grind up my own almonds to make the almond meal/flour. They were just as delicious with a little less color. I think next time I will use a different bean flour instead of soy flour to see how it turns out.

  12. Jan, good to know it will work with garbanzo flour! Did you use any wheat flour at all, or all garbanzo flour?

  13. These muffins are fantastic! I had all the ingredients on hand,except almond flour. I had almonds on hand and could have made almond flour, but looking around I had some Bob's Mill Garbonzo Bean Flour in the fridge and decided to experiment. SUCCESS! The muffins baked up perfectly and the texture was slightly dense. Hubby and I loved the taste and have decided this recipe is a keeper. I also have pictures.

  14. In case you are looking for yet another variation for these muffins (love, love, love them- so glad I found them on your site), I sometimes use soy chorizo, jalapeños (fresh, but I'm sure the canned ones would be fine too), and cotija cheese instead of the parmesan. ¡Qué rico!

  15. These are absolutely delectable. I made them with soy flour instead of the white wheat flour. I did not have Parmesan cheese so I opted for sliced swiss cheese I shredded myself. I also omitted the meat. I love bacon, but when made with certain dishes, it has a tendency to become almost raw in texture–this is gross for me. Thank you so much for the recipe.

  16. They will definitely last for quite a few days in the fridge. I would just refrigerate instead of freezing. (I used to freeze egg dishes like this, but now I prefer them when they haven't been frozen.)

  17. This looks fantastic! I'm going to a friends house for the weekend. Do you think these would last for a few days if I made them ahead of time? (make them on Fri, eat on Sun?) Do you think they would freeze ok? Would be great to make these up for the week.

  18. Mandy, so glad you like the recipe. I used to eat these in the car on the way to work!

  19. Yeah! This is EXACTLY the breakfast muffin recipe I was looking for! Thanks for the trial and error to find the perfect combo.

  20. Ooh this looks yummy. I must try it. Thanks for the recipe!!