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.

PIN the Breakfast Muffins with Bacon to try them later!

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

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 Amazon.com and affiliated sites. As an Amazon Associate, I earn from qualifying purchases.

Leave a Reply

Your email address will not be published. Required fields are marked *

    47 Comments on “Cottage Cheese Breakfast Muffins with Bacon”

  1. Lisa, I honestly don’t know if arrowroot would substitute for flour in a baked item like this, but Heidi did mention you could use soy flour. I think you could make this without the flour too, but it would be a bit more dense. Let us know if you try it.

  2. could you replace the flour with arrowroot powder?

  3. uclafan11, I’m not sure about substituting other types of flour for almond meal. The almond meal is there for people who are using this as part of a diet where you’re not eating white flour or corn meal. If you don’t care about that you could try substituting one of those, but I haven’t tried it. I’m not enough of a baking expert to really make any recommendations about what would work.

  4. Hi there – I do not like almonds or any other nuts really. Is there any substitute for the almond meal? Thanks!

  5. I can’t eat cottage cheese unless it is in a cooked meal – go figure. Regardless, this looks great! I will be trying this one for sure.

  6. I am sold! This is on our menu for this weekends breakfast. Thanks for the great recipe.

  7. These look and sound really good! Cottage cheese would probably go really well in a muffin. I will have to try these.

  8. Oh–that’s the kind of thing after my heart! I would have a hard time eating just one. Cottage cheese improves any bread recipe. And thanks for mentioning my muffins! 🙂

  9. Yum!!! Bacon and cheddar, one of my fav combinations. And I love that you used cottage cheese. These sound fantastic!

  10. Stop, stop, you’re killing me here! That combo of ingredients sounds completely irresistible and muffins are the one thing I am happy to bake on a regular basis (everything else just looks like too much hassle!). Thanks for sharing that recipe – and I agree that crisp bacon is the way forward 🙂

  11. These are the perfect snack, Kalyn – and I also love crisp bacon, it’s the best way of having it, imho!

  12. my god these look good! i rarely follow other peoples recipes closely but i am totally making these with a slight variation… like leaving some of the fat in the bacon. 😉

  13. Lydia, how funny. I never thought of Bob’s Red Mill as being anywhere but Wild Oats or some other overpriced store, so snap it up if you can get a bargain!

    Peter, could be good for any meal, absolutely!

    Maria and Margot, good reminder because I’m sure this will still taste great without the bacon. Also Heidi’s vegetarian version was delicious.

    Katie, bran flakes are also good, in a different way, but these are really tasty!

    B – you’re so welcome, and it reminds me that I need to check whether my flourless peanut butter cookies are gluten free.

    Lucy, how funny. I think my blogger outfit will be a hit with the parents, who are very aware that I’m a food blogger. With the kids, not sure if they will get it, but at least I’ll be comfy at school!

  14. Kalyn, this is a great recipe (I missed Heidi’s…not quite sure how that happened).

    I’m also here to say that your comment on Susan at The Well Seasoned Cook’s Halloween post, about your seasonal outfit? MADE MY DAY!


  15. oh thank you for putting in a gluten-free option on this one. it’s quite challenging to figure the gluten-free thing on my own! i can’t wait for yumminess!

  16. Those look wonderful! I really need to get out of my Bran Flakes and O.J. rut… There’re so many much tastier things in the world.
    Maybe I’ll be inspired to try these…

  17. Kalyn, the look absolutely delicious. I will try to make them without bacon (I don’t eat red meat) if I only get almond meal…

    Enjoy your day, Margot

  18. Cottage cheese is a staple in my diet, I love it. I will for sure try these muffins…minus the bacon:)

  19. I can see myself having these as part of a dinner too!

    I too “cooK’ my bacon in the microwave. A great way to get crispy bacon AND leave the fat behind.

  20. These sound absolutely delicious. I’ve been finding Bob’s Red Mill products in our Ocean State Job Lot stores, of all places! They seem to have the entire product line, so I’m off to get some almond meal.