Kalyn's Kitchen

Cottage Cheese Breakfast Muffins with Ham and Cheddar (Video)

Cottage Cheese Breakfast Muffins with Ham and Cheddar are perfect to make on the weekend and eat all week for a quick breakfast. These tasty muffins have a tiny amount of flour, but they’re still very low in carbs. See notes below to switch out the flour for a version that’s Keto and Gluten-Free!

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Cottage Cheese Breakfast Muffins with Ham and Cheddar finished muffins on serving plate

Back in the days when I had to rush out the door to go teach school every day, easy grab-and-go breakfasts were a must. I made my regular Egg Muffins over and over, (and I confess, I’d eat them in the car on the way to work.) Then I discovered high protein breakfast muffins with cottage cheese and came up with several variations of this tasty easy breakfast, including these Cottage Cheese Breakfast Muffins with Ham and Cheddar. Imagine a biscuit married an omelet and they had a child, but the child got a few more omelet genes than biscuit genes; that’s what these tasty muffins are like.

Now I’m more likely to eat breakfast in front of the computer than behind the steering wheel but it still feels like it’s hard to sit down and eat a proper breakfast. Even if your mornings are more relaxed, you’ll love these easy cottage cheese muffins with ham and cheddar for a breakfast muffin with a delightful taste and texture.

What ingredients do you need for this recipe?

  • finely diced ham
  • grated sharp cheddar
  • green onions
  • cottage cheese
  • grated Parmesan
  • White Whole Wheat Flour (affiliate link), or see Keto and Gluten-Free options below
  • Almond Flour (affiliate link)
  • baking powder
  • salt
  • eggs
  • water

How can you make this recipe Keto and Gluten-Free?

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?

Check out Low-Carb Muffins and Breakfast Muffins for more tasty muffins to eat for breakfast! And you can use Low-Carb and Keto Grab and Go Breakfasts for more breakfasts to eat on the run!

Cottage Cheese and Egg Breakfast Muffins with Ham and Cheddar process shots collage

How to make Cottage Cheese Breakfast Muffins with Ham and Cheddar:

(Scroll down for complete printable recipe.)

  1. Cut up ham into small cubes, slice the green onions and measure out the grated cheese.
  2. Combine the cottage cheese, Parmesan, White Whole Wheat Flour or Flaxseed Meal or Hemp Hearts if that’s what you’re using, Almond Flour, baking powder, salt, eggs, and water in a bowl.
  3. Then stir in the diced ham and grated cheese.
  4. Put the batter into large Silicone Baking Cups (affiliate link) that you’ve sprayed with non-stick spray.
  5. Bake at 400F/200C for 25-30 minutes, or until they’re lightly browned on top.
  6. Muffins can be kept in the fridge for several days and reheated in the microwave.
  7. One of these large muffins is a perfect breakfast for me, but you can make smaller ones if you only have small baking cups.

close-up photo of Cottage Cheese Breakfast Muffins with Ham and Cheddar

More Easy Breakfast Recipes from Kalyn:

Egg Muffins for a Grab-and-Go Breakfast
Bacon Frittata with Two Cheeses
Almond Flour Pumpkin 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 Ham and Cheddar finished muffins on serving plate

Cottage Cheese Breakfast Muffins with Ham and Cheddar

Yield 6 large muffins
Prep Time 10 minutes
Cook Time 30 minutes
Total Time 40 minutes

Cottage Cheese Breakfast Muffins with Ham and Cheddar  are perfect to make on the weekend and eat all week for a quick breakfast.


  • 1/4 cup finely diced ham (see notes)
  • 1/2 cup grated sharp cheddar
  • 2 T sliced green onions
  • 2/3 cup cottage cheese
  • 1/4 cup grated Parmesan
  • 1/4 cup white whole wheat flour (see notes)
  • 2/3 cup almond flour
  • 1 tsp. baking powder
  • 1/4 tsp. salt
  • 4 eggs, beaten
  • 3 T water


  1. Preheat oven to 400 F. Spray large Silicone Baking Cups with non-stick spray or olive oil, or use foil muffin cups. (I would spray those too.)
  2. Dice the ham, slice green onions, and measure out the grated cheese.
  3. In mixing bowl, combine cottage cheese, Parmesan, white whole wheat flour (or Flaxseed Meal or Hemp Hearts), almond meal, baking powder, salt, eggs, and water.
  4. Mix until well combined, then gently stir in ham, sharp cheddar, and green onions.
  5. Divide batter between six muffin cups.
  6. Bake muffins 25-30 minutes or until lightly browned on top and set. (If you’re going to be microwaving, I would bake about 25 minutes, for eating immediately I would use closer to 30 minutes.)
  7. Muffins can be refrigerated and reheated in microwave. Be careful not to microwave too long or they will get tough.


To make a version that's Keto and 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.

I used large Silicone Baking Cups to cook these muffins, and I’d recommend those or foil baking cups for these muffins so they don’t stick to the pan. If you only have metal muffin pans, spray well with non-stick spray or you’ll have a hard time getting the muffins out of the pan! If you have smaller silicone baking cups you can make 12 small muffins instead.

You could use turkey ham if you prefer.

Recipe adapted from Cottage Cheese Muffins at 101 Cookbooks, original recipe by Rose Elliot.

Nutrition Information:



Serving Size:


Amount Per Serving: Calories: 265Total Fat: 18gSaturated Fat: 6gUnsaturated Fat: 10gCholesterol: 154mgSodium: 566mgCarbohydrates: 9gFiber: 2gSugar: 1gProtein: 17g

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 Ham and Cheddar square image of cooked muffins on serving plate

Low-Carb Diet / Low-Glycemic Diet / South Beach Diet Suggestions:
Use white whole wheat flour, lean ham, low-fat cottage cheese, and low-fat cheese if you’re making these breakfast muffins for the original South Beach Diet. With those choices, this would be a good breakfast for phase 2 or 3. See the notes in the recipe for using Flaxseed Meal or Hemp Hearts to replace the flour for a version that’s Keto and Gluten-Free. 

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.

Historical Notes for this Recipe:
This recipe was posted in 2007 and I’ve been making them regularly since then! The recipe was updated with better photos in 2015 and it was last updated with more information and a Keto and Gluten-Free option in 2021.

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    88 Comments on “Cottage Cheese Breakfast Muffins with Ham and Cheddar (Video)”

  1. I make this recipe often, I often sub chicken sausage for the ham and add veggies like spinach and mushrooms Its a great recipe and they reheat great without having that sponge-ey texture a lot of egg muffins can get.

  2. These muffins are super yummy, my husband and daughter love them so much 🙂
    Do you know if I can freeze them please?

    • I wish I could answer but I haven’t frozen them. I don’t like things with eggs frozen (because they release a lot of liquid when they thaw) but in these muffins I think the other ingredients might make it so they would work. If you do try it, I’d love to hear how it works out, thanks!

  3. Pingback: Breakfast on the Go - The Nerdy Cajun Chef

  4. These are really good. I made them for my brother in law who is diabetic. I omitted the almond flour (because I did t have any) and added a drained can of green chilies. The texture is really nice and they taste awesome. Thanks for the recipe!

  5. Hi Kalyn ~ Can you please recommend a replacement for the wheat flour? I don’t metabolize grains very well *at all* but the rest of this recipe looks amazing! Should the almond flour be increased to provide the density needed since the wheat flour won’t be used? Trying to find good alternatives before the baking begins! 😉

    • I used quinoa flakes instead of flour for a gluten-free version of this recipe. I will add that link to the post; hope you enjoy!

  6. Would it be okay to make these with bacon and cheese? Thank you.

  7. These might possibly be the new favorite around here. So delicious.

  8. It's nice to be able to eat breakfast somewhere other than behind the wheel of your car, but these are definitely the perfect grab-and-go breakfast for work days.

    • Yes, hopefully my days of eating in the car are mostly over, but these are a great recipe for people who rush out of the house in the morning.

  9. Yummy! I would love such muffins for breakfast!

  10. Kendra, truthfully I don't really know for sure. I'd probably eat them but I hesitate to advise you to since I don't really know.

  11. Hey! I love these muffins and have been making them over the past 2 months. My husband had a couple this morning and accidentally left them out on the counter for a couple hours, are the rest still okay to eat or should I toss them? Thanks!

  12. Michelle, so glad you are enjoying the recipe. I think you inspired me to make these for my breakfast the next few days. And thanks for sharing your tips!

  13. I've made this recipe twice now, and I absolutely love it!! I love breakfasts that I can make once, then reheat throughout the week! I've made just slight variations, and I'll write them in case anyone's curious.

    1- I've used almond flour and almond meal (the first time I could only find the flour, then I found the meal at Trader Joe's and used that), and both worked. I'd say they're interchangeable here! I did use 1/2 cup instead of 2/3.

    2- I skipped the Parmesan and it turned out fine (my Parmesan had gone bad, but it was just as delicious with only cheddar!).

    3- As far as baking info, I made this using my jumbo silicone muffin pan (lightly greased with butter), and it was perfect. Each muffin uses 6 tbsp of egg mixture (which is 2 scoops of my largest cookie scoop). I bake them for 27 minutes, and reheat them (from cold) for 30 seconds.

    Thank you for sharing this great recipe! I'll make this again & again! 🙂

  14. Almond meal is a little more coarsely ground than almond flour, but both will probably work in this.

  15. Cant wait to try this one… looks super yummy!! I am assuming almond mill is same as almond powder…

  16. Jen, thanks for sharing that. I saw Gluten-Free flour at Costco! So it really is widely available now.

  17. Made these yummy egg muffins GF by using 1/4 C. of GF flour blend and they came out great. Would like to experiment with some healthier GF options, but will have to think about it a bit. Be careful not to add more salt than Kalyn has wisely suggested. I though it sounded a little light on the salt for my taste, but wasn't thinking about the ham or salt in the cheese and mine were a little over the top.

  18. Rick if you look under Frequently Asked Questions in the row of tabs at the top, there is a link for Calorie Count where you can enter the recipe and number of servings and it will calculate the nutritional information for you.