Cottage Cheese Breakfast Muffins with Bacon have egg, Parmesan, almond flour, and a tiny bit of white whole wheat flour. These breakfast muffins are low in carbs, but see suggestions below if you want to replace the flour for a version of cottage cheese muffins that’s Keto and gluten-free.

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Cottage Cheese Breakfast Muffins with Bacon shown on serving plate

Definitely these Cottage Cheese Breakfast Muffins with Bacon are one of my long-time favorites for a make ahead breakfast idea! When I spotted the idea for cottage cheese egg muffins online years ago, I loved the idea of a high-protein muffin with cottage cheese, eggs, Parmesan, and almond meal, and just the tiniest bit of flour.

And when I tried that recipe I discovered that the almond flour and tiny bit of flour gave these cottage cheese muffins a nice texture that was different than the Keto Egg Muffins I’d been making for years. And these muffins with cottage cheese  were definitely a success! And even with the small amount of flour, there are only 7 net carbs per muffin, and 15 grams of protein!

Since I first posted this recipe I’ve made these delicious breakfast muffins over and over to keep in the fridge for a grab-and-go breakfast. And these tasty high protein breakfast muffins have been a hit with everyone who tries them! I hope you’ll try this recipe that’s been one of my absolute favorites for years! 

What ingredients do you need for this recipe?

(This is ONLY a list of ingredients for the recipe; please scroll down for complete printable recipe. Or if you use the JUMP TO RECIPE link at the top of the page, it will take you directly to the complete 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

Want cottage cheese muffins that are 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 these cottage cheese egg muffins. But if you need a version that’s gluten-free or Keto I’d recommend replacing the flour with Flaxseed Meal (affiliate link) or Hemp Seeds (affiliate link), or maybe a combination of both those. There are also a number of brands of Keto Flour (affiliate link) on the market which I am guessing would work fine in this recipe. And there’s also a delicious flourless gluten-free breakfast muffin on the blog that was partly inspired by this recipe.

Want more ideas for cottage cheese muffins like these?

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!

More Ideas for Egg Muffins and Breakfast Muffins?

Check out my post with Low-Carb Muffins and Breakfast Muffins for lots more tasty muffin ideas to make for breakfast!

Cottage Cheese Breakfast Muffins with Bacon process shots collage

How to Make Cottage Cheese Breakfast Muffins with Bacon:

(This is ONLY a summary of the steps for the recipe; please scroll down for complete printable recipe. Or if you use the JUMP TO RECIPE link at the top of the page, it will take you directly to the complete recipe.)

  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, baking powder, 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 Breakfast Muffins with Bacon, six muffins on serving platter

More Low-Carb High Protein Muffin Recipes:

Weekend Food Prep:

This recipe for Cottage Cheese Breakfast Muffins 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 shown on serving plate
Yield: 6 muffins

Cottage Cheese Breakfast Muffins with Bacon

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 low-carb breakfast muffin! See suggestions in the recipe if you need a version that's gluten-free.

Ingredients

  • 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

Instructions

  1. Preheat oven to 400F/200C. Spray silicone baking cups (affiliate link) lightly with olive oil or non-stick spray.
  2. Microwave bacon until crisp and then crumble it. (I use Costco pre-cooked bacon which made this quick.)
  3. Thinly slice green onions.
  4. In mixing bowl, combine cottage cheese, Parmesan cheese, white whole wheat flour, Almond Flour (affiliate link), baking powder, salt, water, and beaten egg. Mix well.
  5. Gently mix in crumbled bacon and green onion, until well distributed in batter.
  6. Fill muffin cups 3/4 full with cottage cheese and egg mixture.
  7. Bake 25-30 minutes, or until muffins are firm and lightly browned.
  8. Serve hot or room temperature.

Notes

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, and I think a gluten-free flour mix would also work.

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 havenโ€™t tried freezing them, but I would imagine they will freeze well.

Recipe adapted from Sundried Tomato Cottage Cheese Muffinsย by Rose Elliot, featured onย 101 Cookbooks.

Nutrition Information

Yield

6

Serving Size

1

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.

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square image of Cottage Cheese Breakfast Muffins with Bacon on serving platter

Low-Carb Diet / Low-Glycemic Diet / South Beach Diet Suggestions:
These cottage cheese muffins are 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. The 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 you could use turkey bacon if you prefer. 

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 Kalynโ€™s Kitchen on Pintereston Facebookon Instagramon TikTok, or on YouTube to see all the good recipes Iโ€™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 2024.

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