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Home / Recipes / Low Carb Breads

Keto Breakfast Muffins with Cottage Cheese

By Lisa MarcAurele · Apr 10, 2025 · 68 Comments

12.2K shares
Jump to Recipe
cottage cheese keto breakfast muffins

These easy keto breakfast muffins with cottage cheese are a tasty, satisfying breakfast! You can make these low carb eggs and bacon muffins ahead of time and enjoy them all week.

keto breakfast muffins with cottage cheese pintrest image
Article Index
  • Why use cottage cheese?
  • How to make muffins with eggs and bacon
  • Other easy low carb breakfast recipes
  • Recipe

Pre-made breakfast options are great when you don’t have time to cook in the morning.

Whether you plan to eat at home or take breakfast to work, it will be much healthier than going through the drive thru.

The good news is that there are plenty of tasty, easy options out there. These bacon, egg, and cheese muffins are one of my favorites!

Why use cottage cheese?

You may be surprised to see that the batter includes cottage cheese. This is my secret ingredient for perfect muffins.

In the past, I’ve tried keto breakfast muffins with almond flour that turned out dry. But cottage cheese muffins turn out perfectly soft and moist! 

Add in the bacon, egg, and cheese, and you have yourself a super tasty, filling breakfast.

This recipe is simple to prep and can be made ahead of time for fast breakfasts during the week. Each of these bacon, egg, and cheese muffins is about 200 calories and 2 net carbs. 

Grab one for a snack or two for a filling meal!

breakfast cottage cheese muffins

How to make muffins with eggs and bacon

This recipe is as simple as mixing together the ingredients and baking in the oven. You’re only a few steps from a full week of low carb breakfast muffins!

Before starting, you’ll want to cook up 3 strips of bacon until crispy. Make sure to blot them so the extra grease doesn’t affect the texture of the muffins.

Prep the batter

  1. In a mixing bowl, combine the cheeses, flours, baking powder, salt, water, and beaten eggs until well combined.
  2. Stir in the crumbled bacon and shredded cheddar.
before baking

Baking the batter

  1. Spray or grease the cups of a 12-muffin tray.
  2. Fill each muffin cup until about ½ to ¾ full.
  3. If you want, you can sprinkle extra cheddar cheese on top.
  4. Bake the muffins for about 25-30 minutes or until they are firm and lightly browned.

Now you have delicious keto breakfast muffins ready for the week!

after baking

How to store cottage cheese muffins

This recipe isn’t just easy to make. It’s also easy to store!

Simply place your bacon and egg muffins in an airtight container in the refrigerator. They should last for about a week.

When you’re ready to enjoy one, you can reheat, or eat it cold straight from the refrigerator. That’s what I usually do, and they’re delicious!

If you want your muffins to last longer, you can store them in the freezer instead.

Keto breakfast muffin variations

These egg, cheese, and bacon muffins can be enjoyed a few different ways.

  • Different fillings: You could add veggies, use a different cheese, or try a different protein! One reader said that ham, mushrooms, and green onions turned out very tasty.
  • Substitute cottage cheese: If you don’t have cottage cheese on hand, you could substitute for ricotta or cream cheese.
  • Dinner rolls: To make a side for your main course, simply omit the bacon and you’ll have perfect dinner rolls. Or, keep the bacon, and they’ll be dinner rolls with a twist!

Have you tried any other low carb breakfast muffin keto recipes? Let us know in the comments below!

cottage cheese low carb keto breakfast muffins

Other easy low carb breakfast recipes

Looking for more grab-and-go breakfasts that you can prep in advance? Check out a few of these favorites:

  • Paleo Egg Casserole is packed with flavor and packed with healthy veggies!
  • Almond Flour Keto Scones are bursting with cranberries and sweet orange flavor for a tasty grab-and-go breakfast.
  • The Muesli Keto Cereal Recipe is a perfect paleo option that’s loaded with whole food ingredients and no added sugar.
  • Banana Bread with Coconut Flour is delicious, low-carb, gluten-free, and perfect for any time of day!
  • Fathead Dough with Coconut Flour makes a tasty low-carb version of a traditional bagel. They’re great with cream cheese!

Follow us on FACEBOOK, PINTEREST, and INSTAGRAM for even more tasty keto-friendly recipes!

Recipe

keto cottage cheese breakfast mufins

Keto Breakfast Muffins

4.91 from 21 votes
These tasty low carb bacon egg and cheese muffins can be made ahead for a week of breakfasts on the go. Much healthier than the fast food chain sandwiches.
Prep Time:10 minutes mins
Cook Time:30 minutes mins
Total Time:40 minutes mins
Course: Breakfast
Cuisine: American
Diet: Gluten Free
Print Pin Review Recipe Save Recipe View Collections
Servings: 12
Calories: 197

Video

Ingredients

  • ⅔ cup cottage cheese
  • ½ cup grated parmesan cheese
  • ¼ cup coconut flour
  • ⅔ cup almond flour
  • 1 teaspoon baking powder
  • ½ teaspoon salt
  • 3 tablespoons water
  • 5 eggs beaten
  • 3 strips no sugar bacon cooked until crisp, fat blotted with paper towel, then crumbled
  • ½ cup cheddar cheese shredded
US Customary - Metric

Instructions

  • Preheat oven to 350°F. Spray or grease muffin cups.
  • In mixing bowl, combine cottage cheese, parmesan cheese, coconut flour, almond meal, baking powder, salt, water, and beaten egg. Mix in crumbled bacon and cheddar cheese.
  • Fill muffin cups ½ to ¾ full. Sprinkle muffin tops with additional shredded cheddar cheese, if desired. Bake 25 -30 minutes, until muffins are firm and lightly browned. Can be served hot or at room temperature.

Notes

You can easily change the taste of these muffins by using a different cheese or substituting another meat like ham for the bacon. 
Ricotta cheese is a great sub for cottage cheese on hand.

Low Carb Sweeteners | Keto Sweetener Conversion Chart

Nutrition

Serving: 1muffin | Calories: 197 | Carbohydrates: 4g | Protein: 15g | Fat: 14g | Saturated Fat: 6g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 3g | Cholesterol: 100mg | Sodium: 600mg | Potassium: 84mg | Fiber: 2g | Sugar: 1g | Vitamin A: 300IU | Calcium: 280mg | Iron: 1.1mg

Additional Info

Net Carbs: 2 g | % Carbs: 4.1 % | % Protein: 30.9 % | % Fat: 64.9 % | SmartPoints: 6
Values
Array
(
    [serving_size] => 1
    [calories] => 197
    [carbohydrates] => 4
    [protein] => 15
    [fat] => 14
    [saturated_fat] => 6
    [polyunsaturated_fat] => 1
    [monounsaturated_fat] => 3
    [cholesterol] => 100
    [sodium] => 600
    [potassium] => 84
    [fiber] => 2
    [sugar] => 1
    [vitamin_a] => 300
    [calcium] => 280
    [iron] => 1.1
    [serving_unit] => muffin
)

Notes on Nutritional Information

Nutritional information for the recipe is provided as a courtesy and is approximate only. We cannot guarantee the accuracy of the nutritional information given for any recipe on this site. Erythritol carbs are not included in carb counts as it has been shown not to impact blood sugar. Net carbs are the total carbs minus fiber.

Copyright

© LowCarbYum.com - Unauthorized use of this material without written permission is strictly prohibited unless for personal offline purposes. Single photos may be used, provided that full credit is given to LowCarbYum.com along with a link back to the original content.

First Published: August 23, 2010... Last Updated: April 9, 2020

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Reader Interactions

Comments

  1. betsy

    January 06, 2025 at 7:39 am

    4 stars
    haven't made them yet -- anyone know if I could add whey protein powder to the batter for some additional protein?

    Reply
  2. Melanie

    October 04, 2023 at 1:28 pm

    5 stars
    So good and moist! My go to breakfast

    Reply
  3. Debbie Gertner

    July 11, 2023 at 10:24 am

    5 stars
    Delicious I made these with following adjustments: 3 whole eggs and 7-8 Tablespoons liquid egg whites, finely grated parm., two round Turkey sausage patties instead of bacon and baked in well greased large heart shaped muffin tins and topped with sharp cheddar. I did omit the salt. They turned out delicious:)
    I like the idea of trying them without the sausage to serve as basic muffin with meals as suggested and also I may try baking them in a square pan if I find myself in a rush! Will add to my regular rotation

    Reply
  4. Terry

    September 01, 2022 at 10:39 am

    The introduction says to bake at 400 F. The recipe says 350 F. Which baking temperature is correct?

    Reply
    • Lisa MarcAurele

      September 04, 2022 at 12:48 pm

      It's 350°F

      Reply
  5. Martine Couture

    August 15, 2022 at 8:07 am

    5 stars
    So so good and satisfying!
    I tweeted my second batch by lining my cups with Mr. Tortilla wraps...

    Reply
  6. Clau Delgadillo

    November 22, 2021 at 11:15 am

    Thank you very much, your recipes are very delicious thanks for sharing

    Reply
    • Lisa MarcAurele

      November 22, 2021 at 8:35 pm

      You're welcome. Enjoy these cottage cheese muffins!

      Reply
  7. BJ

    September 03, 2021 at 5:02 pm

    For a one/two person household, it is so difficult to divide up ingredients for this delicious recipe. Does it freeze well?

    Reply
    • Lisa MarcAurele

      September 06, 2021 at 9:18 am

      These muffins do freeze well if you want to store the leftovers in the freezer. They should keep frozen for at least 3 months.

      Reply
  8. Diane

    September 03, 2021 at 3:58 pm

    What can I substitute the coconut flour with? I hate the taste of that stuff.

    Reply
    • Lisa MarcAurele

      September 06, 2021 at 9:17 am

      You could try using oat fiber or additional almond flour.

      Reply
  9. DOREEN S Shallow

    June 13, 2021 at 3:59 pm

    Thank you, Lisa, so much. I use this delicious waffle recipe to make buns for my burgers, and I say they were amazing. I had to use 2 tablespoons and 1/2 tablespoon instead to have fluffier waffles.

    Reply
    • Lisa MarcAurele

      June 15, 2021 at 11:13 am

      Doreen, this is a muffin recipe. Are you using these to make buns or are you using one of the waffle recipes?

      Reply
  10. Glenda

    January 22, 2021 at 1:35 pm

    5 stars
    What a simple and tasty start to the day! I'm always looking for quick breakfast ideas. These look yummy!

    Reply
  11. Vickie Johnson

    August 24, 2020 at 11:20 pm

    made these yummy Muffins again yesterday and added 1/4 tsp chilli powder, 1/2 tsp cumin and 1/4 cup chopped black olives wow they're sensational!

    Reply
  12. Vickie Johnson

    August 07, 2020 at 10:34 pm

    5 stars
    I just made these Breakfast Muffins so yummy, next time I will experiment with some chilli and cumin or mixed herbs

    Reply
  13. Sharon

    June 24, 2020 at 2:24 pm

    5 Stars!! These taste so good. I was a added some green onion and pepper. Will definitely make these on a regular basis.

    Reply
  14. TerryF

    May 07, 2020 at 3:09 pm

    4 stars
    These had a great texture and taste, but I found them really salty. Next time I would not add the salt as there is plenty already in the cheese and bacon. Thanks for the recipe!

    Reply
    • Oksana Voskresenskaya

      May 17, 2020 at 1:59 pm

      Made them today. The taste is and the texture. But they all stuck to the parchment paper muffin cups. Which ones do you use so they do not stick to them?

      Reply
      • Lisa MarcAurele

        May 17, 2020 at 2:34 pm

        I use silicone cupcake liners as they work much better than parchment paper and are reusable.

  15. LindaHC

    April 19, 2020 at 1:45 pm

    5 stars
    Just made these this morning and they are fantastic!! I added 2-3 Tbls. of chopped green onion, microwaved in 1 Tbls. butter, in bottom of bowl before mixing all the ingredients in. Otherwise I followed the recipe as written. They were perfect. I can't wait to try them with different seasonings and cheeses. Thanks for the recipe!!

    Reply
  16. Laurel Lovelace

    April 16, 2020 at 8:43 am

    Regarding the Parmesan cheese. Is that the heavy powdered kind, or the light fluffy microplaned kind, or the coarsely grated kind....? Pretty big difference between them. Thanks

    Reply
    • Lisa MarcAurele

      April 16, 2020 at 9:23 am

      I use the shredded kind which I believe is what you are referring to as coarsely grated.

      Reply
  17. Sue

    April 13, 2020 at 12:04 pm

    Can I use all Almond Flour??

    Reply
    • Lisa MarcAurele

      April 14, 2020 at 7:45 am

      For this recipe, it should be okay, but texture won't be as spongy.

      Reply
  18. Angela

    April 02, 2020 at 8:57 am

    Can I make this without the muffin pan? Bake it in a 9 × 9 or 8 × 8 bakeware? And then cut them into squares or slices? Depending on if it's a square pan or Round? And if so how would I calculate the carbs or would they remain the same?

    Reply
    • Lisa MarcAurele

      April 02, 2020 at 11:12 am

      The carbs would remain the same if you cut them into 12 slices which is what the nutritional data is based off of. Any pan should work as long as you adjust baking time.

      Reply
  19. Lorraine

    September 21, 2018 at 2:24 pm

    5 stars
    Just made these muffins... again.. better than ever... put in ham, mushrooms and green onions.. perfect!.. thanks so much for your recipes

    Reply
    • Lisa

      September 22, 2018 at 3:17 pm

      Great add-ins!

      Reply
  20. Lorraine

    August 25, 2018 at 1:16 pm

    5 stars
    Love your recipes... I've made several.. all keepers

    Reply
    • Lisa

      August 26, 2018 at 5:00 am

      Thanks for giving the recipes a try! I'm glad they are working out for you. 🙂

      Reply
  21. saltyfish

    February 11, 2018 at 7:31 am

    Hi there! I just found your site and it looks so amazing. One question about the flours. I've never cooked with the coconut flour and am allergic to tree nuts so the almond flour is out. Can I use all coconut flour or do you have another suggestion? Thanks.

    Reply
    • Lisa

      February 11, 2018 at 12:09 pm

      For this recipe, you'll need to use a seed flour in place of the nut flour. Something like sunflower seed flour or flax meal should work.

      Reply
  22. Nathalie

    October 17, 2017 at 3:17 am

    Can you replace the cottage cheese with something else?

    Reply
    • Lisa

      October 17, 2017 at 6:59 am

      You could use ricotta or cream cheese.

      Reply
  23. Vivian

    June 04, 2017 at 8:16 am

    5 stars
    Like the food.

    Reply
    • Lisa

      June 04, 2017 at 9:44 am

      Thanks Vivian!

      Reply
  24. hada

    April 27, 2017 at 12:45 pm

    what can I use instead of cottage cheese?

    Reply
    • Lisa

      April 27, 2017 at 1:11 pm

      You could try ricotta or mozzarella. Cream cheese or sour cream might be okay too.

      Reply
  25. Kurt W

    April 20, 2017 at 8:40 am

    We make these all the time and love them with a few additions to the recipe. I add 4 Tbs of melted butter with about 2 Tbs of finely chopped onion sautéed in the melted butter.

    Reply
    • Lisa

      April 20, 2017 at 4:19 pm

      Love the added butter!

      Reply
  26. Kurt

    March 22, 2017 at 8:21 pm

    Love these with a minor addition of a half a stick of melted butter (4Tbsp)and a quarter cup of onion, lightly sautéed in the melted butter. YUM!

    Reply
    • Lisa

      March 23, 2017 at 5:49 am

      Definitely sounds like a yummy add!

      Reply
  27. Emily

    March 01, 2017 at 12:24 pm

    Do you know the calories per muffin? Thinking about making these for next week but I like to have an estimate of calories so I can fit it into the rest of my mealprep. Thanks!

    Reply
    • Lisa

      March 01, 2017 at 5:49 pm

      I did a quick calc and it's showing 197 calories per muffin.

      Reply
  28. Connie

    July 04, 2016 at 8:24 am

    5 stars
    Just made these this morning and the recipe is perfect. I wouldn't change a thing. Now excuse me as I start on my second one. lol

    Reply
    • Lisa

      July 04, 2016 at 11:34 am

      Thanks Connie!

      Reply
  29. Joan

    July 03, 2016 at 4:56 pm

    Wondering if these can be frozen??

    Reply
    • Lisa

      July 03, 2016 at 7:06 pm

      They can be frozen after baking if you'd like to save some for easy breakfasts later.

      Reply
      • Joan

        July 03, 2016 at 8:32 pm

        Awesome!! I thought you could but wanted to check. LOVE your recipes!!

      • Lisa

        July 04, 2016 at 11:35 am

        🙂

  30. Teresa Vandiver

    November 30, 2015 at 8:07 pm

    These are so good. I think I've found a new breakfast favorite! Thank you!

    Reply
    • Lisa

      December 01, 2015 at 11:00 am

      You're welcome Teresa! Glad you love them as much as I do!

      Reply
  31. Vonne

    September 01, 2015 at 10:08 pm

    I made these without the bacon just to serve as dinner rolls and they were really good! My kids really ate them up and one of them is a very picky eater! This recipe is definitely a keeper! 🙂

    Reply
    • Lisa

      September 02, 2015 at 5:32 am

      Thanks for sharing how well they came without the bacon! I've made it a couple times as a bread using different flavors of cheese and it was also delicious.

      Reply
  32. Tracy

    February 09, 2015 at 6:42 pm

    What can I use to substitute coconut flour. I am allergic to coconut. Any suggestions that will keep them low carb?

    Reply
    • Lisa

      February 10, 2015 at 3:33 am

      If you do not have any issues with gluten, you can sub it with Carbquik or oat fiber. Otherwise, you could use all almond flour (I'd try about 1 cup total).

      Reply
  33. zandi

    October 14, 2011 at 1:11 pm

    guess my oven is off or i wasnt paying attention mine were a little dry ,my fault i'm sure,but were stll gteat

    Reply
    • Sue

      February 16, 2021 at 11:04 pm

      5 stars
      My first batch came out a little dry, too. Not a problem, though, as I just heated them up with a nice chunk of sharp cheddar on top and they were delicious.

      My second batch I cooked at 350 degrees for 25 minutes and they were just as moist and yummy as Lisa described! I think you have to sometimes tweak recipes a bit to make them work with your appliances.

      Definitely a regular recipe I make, switching up breakfast meats and cheeses. Soooo many options!!! Thank you, Lisa!

      Reply
      • Lisa MarcAurele

        February 17, 2021 at 7:04 am

        Thanks for sharing that. I do think 400°F is too high so I'm changing the recipe to 350. This is a really old recipe and I've since learned that gluten-free baked goods do better at a lower temp.

  34. Ivonne

    September 10, 2011 at 5:37 pm

    WOW These were so awesome, I had two for breakfast today... Thanks so much for sharing these recipes! These were not only easy to make but the end result was way better than I was expecting. Cheers! 🙂

    Reply
  35. Driver

    October 25, 2010 at 3:18 pm

    Keep up the nice text, added to my internet explorer rss.

    Reply
  36. Flavorful World

    September 01, 2010 at 3:40 am

    Looks great. I'm all for any breakfast item that can be made in advance, since I rarely have the time during the work week to make anything elaborate. I'll have to try this one...

    Reply
    • Beef Jerky

      March 19, 2011 at 6:42 pm

      Beef jerky is the most healthful snack food there is, and it is so simple to make I'm really amazed that more folks don't do it.

      Reply
  37. veterinary technician

    August 30, 2010 at 3:53 pm

    What a great resource!

    Reply
  38. fooddreamer

    August 23, 2010 at 9:48 pm

    These look delicious. Coconut flour is crazy stuff, eh? How much moisture it absorbs!
    BTW, the Low Carb Energy bars really are remarkably good. If you are looking for a replacement for the Kashi bars, give these a try! I finished them up over the weekend and was craving more today. Didn't have time to make any but definitely soon.

    Reply
    • Lisa

      August 23, 2010 at 10:30 pm

      I love the coconut flour. It replaces wheat flour well when used with additional egg to compensate for the gluten. I've also added your Dream About Food blog to my blogroll links on this website since you post some great recipes over there.

      Reply
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