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Kalyn's Kitchen

Cottage Cheese and Egg Breakfast Muffins with Bacon and Green Onions

Cottage Cheese and Egg Breakfast Muffins with Bacon and Green Onions have cottage cheese, egg, almond flour, and and just a little white whole wheat flour for a tasty breakfast muffin that’s low-carb and low-glycemic. Use Breakfast Recipes to find more recipes like this one.

Click to PIN Cottage Cheese  and Egg Breakfast Muffins with Bacon!

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

When Heidi Swanson of 101 Cookbooks shared a recipe from Rose Elliot for Cottage Cheese Muffins, 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 decided to experiment and see if I could make a version that was more of a breakfast muffin. And I have to say these Cottage Cheese and Egg Breakfast Muffins with Bacon and Green Onions were definitely a success; since I first posted this recipe eight years ago, 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 carb-conscious 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 gluten-free Egg Muffins. Since then I’ve made several other versions of these delicious cottage cheese filled muffins including a gluten-free version, so you can tell how much I loved them.

Then recently I realized that all these recipes really need new photos if I’m going to entice any of my newer readers to try them! So I made this favorite breakfast treat again and snapped new pictures to show them off a little better. This is still one of my all-time favorite low-carb breakfasts; hope you enjoy!

(Cottage Cheese  and Egg Breakfast Muffins Recipe with Bacon and Green Onions were updated with better photos, September 2015.)

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

Mix together the cottage cheese, Parmesan, white whole wheat flour, almond meal, salt, water, and beaten egg. Then fold in the crumbled bacon and thinly sliced green onion. Fill large muffin cups 3/4 full, bake, and enjoy! (Heidi says you can use soy flour for a gluten-free version, but I haven’t tried that. I did have good success making a similar muffin with Quinoa Flakes though.)

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

One of these muffins is enough for me for a tasty breakfast, and since that’s only 1/2 of a strip of bacon, I don’t feel the least bit guilty about adding a little bacon, but use turkey bacon if you’d like to make them more South Beach Diet approved!

More High Protein Muffin Recipes:

Grab-and-Go Egg Muffins ~ Kalyn’s Kitchen
Double Chocolate Low-Carb Power Muffins ~ All Day I Dream About Food
Flourless Egg and Cottage Cheese Breakfast Muffins ~ Kalyn’s Kitchen
Egg and Cheese Breakfast Muffins with Mushrooms and Thyme ~ The Perfect Pantry
Green Chile and Cheese Egg Muffins ~ Kalyn’s Kitchen
Protein-Filled Quinoa Muffins ~ Sippity Sup

Weekend Food Prep:

This recipe has been added to a new 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 and Egg Breakfast Muffins with Bacon and Green Onions

Cottage Cheese and Egg Breakfast Muffins with Bacon and Green Onions have cottage cheese, egg, almond flour, and and just a little white whole wheat flour for a tasty breakfast muffin!


  • 2/3 cup cottage cheese (regular or low-fat)
  • 1/2 cup grated Parmesan cheese
  • 1/4 cup white whole wheat flour
  • 2/3 cup almond meal (I used Bob’s Red Mill almond meal, you can use 2/3 cup almonds ground in food processor for this, which makes it slightly chunkier)
  • 1 tsp. baking powder
  • 1/2 tsp. salt
  • 3 T water
  • 4 eggs, beaten
  • 3 strips bacon, cooked until crisp, fat blotted with paper towel, then crumbled
  • 3 T thinly sliced green onion (scallions)


  1. Preheat oven to 400 F. Spray silicone baking cups lightly with olive oil or non-stick spray, or use foil muffin liners (I would spray those also.)
  2. In mixing bowl, combine cottage cheese, Parmesan cheese, white whole wheat flour (I’ve used Quinoa Flakes for gluten-free version, and you can use soy flour as well according to Heidi), almond meal (I used Bob’s Red Mill almond meal), 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.


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.

All images and text ©

Low-Carb Diet / Low-Glycemic Diet / South Beach Diet Suggestions:
These Cottage Cheese and Egg Breakfast Muffins with Bacon and Green Onions would be phase 2 or 3 for the South Beach Diet, due to the flour; but these muffins are still low enough in carbs to work for most low-carb diets. I wouldn’t worry about the small amount of bacon here, and the bacon adds a lot of flavor, but use turkey bacon if you prefer. Even with low-fat cheese, 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 the Recipes by Diet Type photo index pages to find more 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.

Nutritional Information?
If you want nutritional information for a recipe, I recommend entering the recipe into Calorie Count, which will calculate it for you.

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49 comments on “Cottage Cheese and Egg Breakfast Muffins with Bacon and Green Onions”

  1. I just made these last night! I followed the recipe exactly! (Except I had to use the parmesan in the green bottle, oops) Super easy! I'm eating one right now and it's really good! Thanks!

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

  3. 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.

  4. 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. I'm not sure you could duplicate the goodness without the almond meal; they give the muffins a nutty taste and add a lot of protein. But if you make them sucessfully with something else, I'd love to know about it.

  5. 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 because I haven't made them without it and I'm not good enough at baking to know what else might work. If you try something that works, I'd love to hear about it.

  6. 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.

  7. 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.

  8. 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?

  9. 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.

  10. 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.

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

  12. 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.

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

  14. 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.

  15. 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!

  16. So glad you enjoyed them and I love knowing it will work with soy flour.

    I chose the South Beach Diet to manage my weight partly because I didn't want to have to calculate the calories, points, or other nutritional information for everything I ate, so I don't have that information.

  17. Would you happen to know the protein, calorie, and fiber content of this recipe?

  18. 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.

  19. 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.)

  20. 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.

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

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

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

  24. 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.

  25. could you replace the flour with arrowroot powder?

  26. 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.

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

  28. 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.

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

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

  31. 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! 🙂

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

  33. 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 🙂

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

  35. 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. 😉

  36. 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!

  37. 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!


  38. 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!

  39. 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…

  40. 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

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

  42. 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.

  43. 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.

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