Keto Cottage Cheese Breakfast Muffins

These keto cottage cheese breakfast muffins are the perfect recipe to make in advance to have breakfast ready to go for the week ahead. Eat them fresh out of the oven or store in the fridge and grab a couple on your way out the door (they’re a fantastic keto breakfasts for on-the-go).

Packed with 9g of protein and only 2g net carbs per muffin, they’re sure to keep you feeling nice and satisfied throughout your morning. The cottage cheese ensures they have a lovely moist texture and full body, plus it adds a good dose of protein to the mix! They’re easily one of my very favorite keto cottage cheese recipes.

Everyone I’ve made these for have loved them – even my picky little nieces and nephews!

keto cottage cheese breakfast muffins still in the tin!

What substitutions can you make to keto breakfast muffins?

The great thing about breakfast egg muffins is that they’re very versatile. You can easily substitute the bacon for diced ham.

Additionally, you can swap the cottage cheese for ricotta cheese, or the cheddar cheese for mozzarella cheese. You could also add any of your favourite vegetables or extra seasonings that you wish. I find that a few bits of cherry or grape tomatoes goes great along with some baby spinach leaves. I often also bolster the base with some finely chopped onion.

How do you keep these keto cottage cheese breakfast muffins from drying out?

Keeping them in an airtight container in the fridge will stop these from getting too dry. If you do leave them out, or find they have dried out for any reason it can be hard to get the moisture back in. In that case, eating them with some condiments does the trick. I love my homemade ketchup or relish, and these go great with either!

How long will they keep in the fridge?

These muffins will last in the fridge for up to 4 days. To reheat, simply warm in the microwave for about 20 – 30 seconds. You can eat them cold too, but I don’t think they’re nearly as yummy that way.

hand holding a keto cottage cheese breakfast muffin

keto cottage cheese breakfast muffins on muffin rack

Keto Cottage Cheese Breakfast Muffins

These are like little bite-size bacon and egg breakfasts! Packed full of protein and low in carbs they're quick, easy and delicious. The whole family will love them!
Prep Time 10 mins
Cook Time 30 mins
Total Time 40 mins
Course Breakfast, Snack
Cuisine American
Servings 12 muffins
Calories 139 kcal


  • 1 12 cup muffin tray
  • 1 Large mixing bowl


  • 2/3 cup Cottage cheese (I use 4 or 4.5% fat)
  • 1/2 cup Cheddar cheese (shredded)
  • 1/2 cup Parmesan cheese (grated or shredded)
  • 2/3 cup Almond flour
  • 1/4 cup Coconut flour
  • 5 large Eggs (whisked)
  • 1 tsp Baking powder
  • 1/2 tsp Salt
  • 3 tbsp Water
  • 3 strips Cooked and crumbled bacon


  • Preheat oven to 350˚F (180˚C). Spray or grease your 12 cup muffin tray. Also heat a frying pan over medium - high heat.
  • Cook the bacon to well done. Blot with paper and then crumble. Put aside.
  • 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


keto cottage cheese breakfast muffin nutrition label
Keyword keto breakfast muffins, keto cottage cheese breakfast muffins