Cheesy Egg Muffins

These Cheesy Egg Muffins are so tender and such a satisfying breakfast. The eggs and cottage cheese mixture combined with all sorts of delicious breakfast ingredients are baked in a muffin pan to make individual portions. These egg muffins are great for meal prepping for the week and freeze really well too.

I discovered this recipe more than a decade ago and have been making different versions of it for my family ever since. These egg muffins are cheesy, tender and are kind of like individual omelets with an endless possibility of fillings, such as sausage, ham, bacon, mushrooms, spinach, tomatoes, peppers, zucchini, broccoli, etc. Today I am sharing two options – Ham and Bacon for one meaty and hearty variation and a vegetarian version with onions, mushrooms and spinach.

Instead of baking these in individual portions, you can bake the egg mixture in a casserole dish. It makes for the most amazingly delicious and beautiful Breakfast Casserole. Serve these for brunch or overnight guests. It’s so easy to put together but looks really spectacular and is always a big hit.

They are also great as leftovers and freeze really well too. Make a big batch, store it in your refrigerator and just reheat in the mornings.

Watch the Video of How To Make Cheesy Egg Muffins


  • eggs – I use large eggs for this recipe.
  • cottage cheese – you can use ricotta cheese or farmer’s cheese instead, although cottage cheese yields the best results.
  • melted butter
  • all purpose flour
  • grated cheese – any cheese that melts well can be used, such as mozzarella, provolone, cheddar, Monterey Jack, Colby, etc.
  • salt and ground black pepper
  • filling options: ham, breakfast sausage or bacon need to be cooked in advance, most vegetables also need to be cooked in advance before adding it to the egg batter. Vegetables: onions, mushrooms, spinach, bell peppers, broccoli, asparagus, zucchini, etc.
  • fresh herbs – chives, green onions, parsley, thyme, etc.

Cottage Cheese in Eggs? Will it taste like cottage cheese? Substitution options for Cottage Cheese

Cottage cheese is the secret ingredient in this recipe that makes the egg muffins or the breakfast casserole extra tender and moist. The cottage cheese will melt into the eggs and you won’t taste the cottage cheese in them. Most people won’t even guess it’s in there.

Instead of cottage cheese, you can also use ricotta cheese or farmer’s cheese. Farmer’s cheese tends to be much drier in texture than cottage cheese, so I suggest adding 1-2 Tablespoons of sour cream, yogurt or milk in addition to the farmer’s cheese.

Why Do the Vegetables Need To Be Cooked First?

Since the egg muffins will be baking in the oven, some people wonder why the vegetables need to be cooked first. Why not add them in raw, save yourself some time and dishes since they’ll be cooked in the oven anyway.

Simply because there is not enough time for the vegetables to cook through. In the time that it takes the muffin batter to bake through, the vegetables will only begin to cook. They will still be raw. Vegetables also have a lot of excess moisture in them, so they will add too much moisture to the egg muffins, so the texture won’t be right. Finally, cooking the veggies first will give them a much more delicious flavor. Sautéing gives them a much deeper and richer flavor. Without cooking the veggies, they will taste bland.

Making the Cheesy Egg Batter

Cheesy Egg Muffins Making the batter tutorial
  • Preheat the oven to 350 degrees Fahrenheit. Line 2 muffin pans with liners. My favorite to use are parchment liners.
  • If you need to cook the fillings, do that first, so that it can cool off slightly before you add it to the egg batter. (Cook the sausage, bacon, onions, spinach, peppers, broccoli, etc. in a skillet until cooked through, then set aside to cool.)
  • In a large bowl, whisk the eggs until they are evenly mixed, then add the rest of the ingredients: cottage cheese, grated cheese, melted butter, all purpose flour, baking powder, salt and pepper. Mix to combine.
  • Add the filling ingredients: chives or other fresh herbs, bacon and ham for the first muffins that I showed in the video. For the second flavor variety, add the cooked onion, mushrooms and spinach. Mix to combine.
  • Scoop out the batter into the lined muffin pans. Bake for about 30-35 minutes.
  • You should have about 22-24 muffins, depending on how much filling ingredients you use and how much you fill the muffin pans.
  • Cool the muffins for about 5 minutes then remove from the muffins pans. Don’t let the muffins cool off in the muffin pans. The condensation on the bottom will make the muffins wet and that’s not tasty.

Ham, Bacon and Chive Muffins:

I usually use leftover bacon for this option, so I don’t have to cook any of the filling ingredients. Cut up the ham, bacon and chives. Add to the egg batter and mix to combine.
Fill the muffin pans and bake for 30-35 minutes.

Spinach and Mushroom Egg Muffins:

This is my absolute favorite option. The veggies in the egg muffins give it such a great flavor and since I really enjoy lots of veggies in my omelets too, I really like these veggie egg muffins and I also like making this into a breakfast casserole too.

  • In a skillet, heat 1/2- 1 Tablespoons of butter or oil and add the chopped onion. Season with salt and pepper, and cook until the onions are tender, on medium heat, for about 5 minutes.
  • Add the sliced or chopped mushrooms, season with salt, pepper and cook for another 5-7 minutes on medium high heat.
  • Meanwhile, squeeze out all the excess liquid out of the frozen spinach, there is A LOT of liquid, and then add to the skillet. Season once more with salt and pepper and cook just for 1-2 minutes, until the spinach is warmed through. If you want to use fresh spinach, cut it up into smaller pieces and add last to the skillet. Cook until the spinach wilts, about 3-4 minutes. Cool to room temperature and then add to the egg batter.
  • Scoop out and bake in the preheated oven for 30-35 minutes.

Storing the Egg Muffins, Freezing and Reheating:

Store the egg muffins in the refrigerator in an airtight container for up to a week.

Freeze in an airtight container or freezer bag for up to 3 months.

You can reheat the egg muffins in the microwave or use a skillet or oven.

For the skillet method: add a splash of water to the skillet, add the muffins, cover and cook on medium low heat until the muffins are warm all the way through. The water won’t make them watery – it will keep them moist and prevent them from burning. The water will create steam in the covered skillet and help to warm them through more evenly and quickly.

Preheat the oven to 400 degrees and place the muffins in the oven, covered. Bake until warmed through, 5-10 minutes.


Cheesy Egg Muffins

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These Cheesy Egg Muffins are so tender and such a satisfying breakfast. The eggs and cottage cheese mixture combined with all sorts of delicious breakfast ingredients are baked in a muffin pan to make individual portions. These egg muffins are great for meal prepping for the week and freeze really well too.

  • Author: Olga’s Flavor Factory
  • Prep Time: 15 mins
  • Cook Time: 45 mins
  • Total Time: 1 hour
  • Yield: 2024 muffins 1x
  • Category: Breakfast



Egg Muffins:

  • 10 large eggs
  • 2 cups cottage cheese (ricotta cheese or farmer’s cheese can be used instead)
  • 3/41 1/2 cups grated cheese (mozzarella, provolone, cheddar, Monterey Jack, Colby, etc.)
  • 4 Tablespoons melted butter, slightly cooled
  • 1/2 cup all purpose flour
  • 1 teaspoon baking powder
  • 1/2 teaspoon salt
  • 1/2 teaspoon ground black pepper1 1/2 cups grated cheese, (mozzarella, provolone, monterey jack, etc.)
  • 12 tablespoons fresh parsley, chives, green onions, minced

Filling Options:

Bacon and Ham 

1/2 lb ham and bacon (You can also use 1/2 lb of sausage instead or in addition to the ham and bacon.)

Spinach and Mushroom:

1/2 – 1 Tablespoon butter or oil, for sautéing the veggies

1 small or medium onion, finely chopped

8 oz mushrooms, sliced or chopped

10 oz frozen spinach, thawed

salt, ground black pepper, to taste



Cheesy Egg Muffin Batter:

  1. Preheat the oven to 350 degrees Fahrenheit. Line 2 (12 cup) muffin pans with muffin liners.
  2. Cook the filling ingredients if they need to be cooked, such as bacon, sausage, onion, mushrooms, spinach, peppers, tomatoes, broccoli, asparagus, etc. Cool slightly.
  3. In a large bowl, whisk together the eggs until they are evenly mixed.
  4. Add the cottage cheese, melted butter, grated cheese, flour, baking powder, salt, pepper and fresh herbs. Mix to combine.
  5. Add the cooled off filling ingredients and mix to combine.
  6. Scoop out the egg batter and fill the lined muffin cups 3/4 of the way or completely full. You will have 20-24 muffins, depending on how much filling you use and how much you fill the muffin cups.
  7. Bake in the preheated oven for 30-35 minutes.
  8. Cool the muffins for about 5 minutes, then remove from the muffins pans.
  9. Store the egg muffins in the refrigerator in an airtight container for up to 1 week or freeze for up to 3 months.
  10. Serve the egg muffins while warm or reheat in the microwave, skillet or oven until heated through.

Spinach and Mushroom Egg Muffin Filling:

  1. In a large skillet, heat up the butter or oil. Add the onion, season with salt and pepper and cook, for about 5 minutes, until tender.
  2. Add the mushrooms, season with salt and pepper and cook for another 5-7 minutes, util the mushrooms are cooked through and slightly golden.
  3. Meanwhile, squeeze out all the excess liquid from the frozen spinach, then add to the skillet. Cook for just 1-2 minutes until heated though, seasoning with salt and pepper as well.
  4. If you want to use fresh spinach, chop it up and add to the skillet last, season with salt and pepper and cook until the spinach is wilted, 2-4 minutes. Cool slightly before adding to the egg batter.

Did you make this recipe?

Share a photo and tag us — we can’t wait to see what you’ve made!

This recipe was originally published on May 4, 2012. I have clarified the instructions and added a video to make it even better. Enjoy!


  • Milana

    Made double today.They were so good !!!! Everybody liked them so much!!!! Will do again !!!!! Thank you for recipe Olga!!! So proud of you!!!!!!

  • Natasha of

    That looks like the perfect breakfast food! This is a great idea for company; make ’em all in one swoop! Thank you!

  • Natasha of

    Oh and I too absolutely love the library. I’ll be happy to re-discover it now that I’m done with classes!!! I miss my novels, I mean cookbooks 🙂

    • Olga K.

      I know what you mean. I remeber feeling like a mountaing fell off my shoulders when I was FINALLY done with nursing school and passed my Boards. Congratulations. Enjoy some time to yourself:)

  • Natalie S

    These look so tasty and easy! Just a quick question – what can I substitute if I am making it for some company and they are vegetarian? If I leave off the sausage, can I add some different veggies?

    • olgak7

      You can use mushrooms, peppers, tomatoes, zucchini, asparagus, etc. Just cook it first by roasting or sautéing before adding to the egg and cheese mixture.

  • Irena

    Hi Olga!
    I’m thinking about making a large batch and freezing them, have you tried doing that? Wondering if they would defrost nicely.

    • olgak7

      Hi Irena! I’ve never tried it, but I don’t see why not. I’ve had great results with egg dishes in the past. I make breakfast burritos with eggs and freeze them. I think these would work well too. Let me know how it turns out.

  • lanchick7

    Olga, thanks so much for this recipe!! I’ve made these puffs 4 times already!!!! and they turn out better and better every time 🙂 I donno what it is about eggs but I always crave them like crazy.. 😉 this last time I omitted the onions and they turned out the best!!! my hubby even commented on how much better he liked them

  • Irina

    These were awsome, thanks Olga for the post. I also froze mine and then defrosted them in my toaster oven for about 4-5 min and they tasted freshly made. Thank You!!!

  • Oksana K

    Made this yuminness two days ago in the evening, then had them with coffee next morning as they were – cold, and they were DELLLLISH!:-P Had 2 with coffee this am too. I used Johnsonville sausage and ricotta cheese, turn out absolutely amazing!!!
    thank you again, for all the great recipes and helpful tips.
    God bless you, girl! 😀

    • olgak7

      I wouldn’t make it the night before, since the batter has baking powder in it, which starts to react as soon as you make the batter. You can prep everything ahead of time, (cook the filling, mix up the cheeses, mix the dry ingredients separately) and the next morning mix it all together. For best results, that’s what I would suggest.

  • Yana

    Made these and absolutely loved them!!! Froze extra ones, they heat up great in the microwave!!! Love your recipies and ideas!!! Thank you so mich for sharing them with us!! I recommended your site to all my friends and family. My mom absolitely loves your site too !!! 🙂

    • olgak7

      Thank you, Yana; I really appreciate that!
      I’m so happy to hear your success stories. It’s such an awesome thing when I hear of other families enjoying our family favorites too.

  • SvetKa

    I tried a half batch with flaky smoked salmon and scallions and it was to die for! Have you tried these with berries instead of savory fillings? Sort of baked syrniki style?

    • olgak7

      The oven temperature is 350 degrees Fahrenheit, Galya. (It’s written at the top; the first line of the recipe instructions. I should write it in at the end too.)

      • Alya

        I ended up grabbing some cottage cheese. They turned out delicious! I made two different batches – bacon/garlic/broccoli and sausage/spinach/eggs. I omitted the parsley and chives and seasoned with black pepper. Very, very tasty. Will become a staple 🙂 thank you!

  • Tzivia

    Mmmmmm these look really way good question if I don’t have ricotta or cottage cheese would it work with the tvorog cheese or sour cream or plain greek yogurt @ a substitute mmmmm egg and cheese what could be better lol

      • olgak7

        Thank you for sharing, Svetka. I have noticed that usually you can use tvorog (farmer’s cheese), cottage cheese or ricotta cheese interchangeably usually works out great in most recipes.

        • Tzivia

          Oh ok so it would work with tvorog cheese such a gr8 cooking and frying cheese for syrniki thanx tons svetka and olya sweeties cheers

  • Svetlana

    Been making these for years, huge fan (and they work with Matzo Meal, too, so I make them for Passover!)
    Wanted to report on a successful filling experiment:
    About 2/3 cups of home-made pesto and 1/2 cup chopped oil-packed sundried tomatoes, *OMIT BUTTER* in the recipe. Kids were fighting over them. 🙂

  • Zoya

    Thank you Olga for all your amazing recipes and inspiration! Do you know what size of a casserole dish would be needed for this and how long to bake? Would a regular pie dish work? Thank you so much.

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