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Breakfast Egg Muffin Cups

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These Breakfast Egg Muffin Cups are a delicious make-ahead breakfast packed full of protein, veggies and is totally customizable! Make them ahead of time, refrigerate or freeze them, and then heat them for a quick breakfast.

a stack of breakfast egg muffin cups with mushrooms and tomato in the background

Breakfast Egg Muffins

I love to make breakfast meals that are filling, quick to make, pack in the nutrition and the leftovers store well! These breakfast egg cups fit every requirement! These egg cups are creamy, warm and perfectly portioned to be filling for kids and adults both!

Ingredients for Breakfast Egg Cups

The ingredients for egg cups are very basic. The add-ins are really the star of the recipe and I have lots of variations for you to try. These are what you will need for the egg base:

  • Eggs – large eggs are best for this recipe
  • Milk – makes the egg cups more rich and a better texture. You can use any type of unsweetened milk
  • Cottage Cheese – Provides extra protein, and flavor. You can use any fat % you like, but try to find small curd.
  • Salt + Pepper – a must for any egg dish!
basic ingredients for breakfast egg cups, eggs, milk, cottage cheese, salt and pepper

Ingredient Variations for Breakfast Egg Cups

This recipe is the best because you can use your favorite add-ins! Here are some yummy combinations you might want try.

Garden Veggie Egg Cups

  • Egg Cup Base
  • Spinach
  • Tomatoes
  • Mushrooms
  • Cheddar Cheese
ingredients for garden veggie breakfast egg cups spinach, tomato, mushroom, cheddar cheese

French Egg Cups

  • Egg Cup Base
  • Green Onion
  • Smoked Gouda Cheese
  • Asparagus
ingredients for french breakfast egg cups, green onion, asparagus, gouda cheese

Meat Lovers Egg Cups

  • Egg Cups Base
  • Diced Ham
  • Crumbled Bacon
  • Crumbled Sausage
ingredients for meat lovers breakfast egg cups, diced ham, crumbled bacon, crumbled sausage

Greek Egg Cups

  • Egg Cups Base
  • Feta Cheese
  • Tomatoes
  • Kalamata Olives
ingredients for Greek breakfast egg cups with feta cheese, kalamata olives and tomatoes

Spanish Egg Cups

  • Egg Cups Base
  • Black Beans
  • Green Bell Peppers
  • Tomatoes
  • Salsa
ingredients for spanish egg cups with salsa, tomato, black beans, green bell peppers

How to Bake Eggs in Muffin Cups

These egg cups take just a few minutes to whip up!

  1. Preheat oven to 375 degrees F. Spray a muffin tin with non-stick spray.
  2. Whisk together eggs in a large bowl. Add cottage cheese, milk, salt and pepper.
  3. Stir in add-ins for whatever type of egg muffin cup you are making.
  4. Pour egg mixture into muffin tin, filling each cup 3/4 of the way full.
  5. Bake for about 25 minutes, until the centers are completely set. The edges will slightly brown.
  6. Allow to cool for a few minutes before removing and serving.
breakfast egg cups uncooked in a muffin tin and then cooked in a muffin tin

Tips for Making the Best Egg Muffins

  • Make sure you whisk the egg base well so that the whites and yolks of the eggs are thoroughly combined. This prevents clumps of egg white getting cooked and not mixing in.
  • Chop and dice the add-ins very small. You want to get an even mix of add-ins with every bite, and chopping things small is the best way.
  • Spray each muffin cup really well with a good non-stick cooking spray. Eggs are notorious for sticking to things, but if you coat the tin well, they shouldn’t stick.
stack of 3 breakfast egg muffin cups

How Do You Store Egg Muffin Cups?

You can store these in the fridge for up to 5 days or in the freezer for 2 months.

To Store: After they are baked, let them cool and then put in an airtight container. You can reheat in the microwave for 30 seconds from the fridge, and 60 seconds from the freezer. I recommend wrapping in a paper towel from the freezer before microwaving to remove extra water and give a better texture when reheated.

Can You Eat Eggs Every Day?

Eggs have gotten a bad reputation over the years because they contain cholesterol.  A large egg contains about 185 mg of cholesterol, and the recommendation from the American Heart Association (AHA) is a limit of 300 mg per day.

So, should you limit your egg intake?  The answer is essentially no.  The recommendation from the AHA can be confusing, and here is why.  It assumes that when you eat more cholesterol from food,  your blood cholesterol increases. But, your body actually doesn’t work that way. The research consistently and reliably shows that the cholesterol you eat has very little impact on how much cholesterol is in your blood.

Your body actually makes its own cholesterol. Lots of it, in fact. Every single day you produce between 1 and 2 grams of it on your own. (That’s 5-10 times the cholesterol in a large egg.) When you eat more cholesterol from foods like eggs, your body produces less of it. And when you eat less cholesterol, your body produces more.  Cholesterol is actually really important in your body. It is in every outer layer of all your cells.  It’s a requirement for growth (in infants and adults). And it’s required for the production of many hormones.

The egg paranoia has been based on the old assumption that eating the yolks will raise blood cholesterol (and increase your risk for artery and heart disease).  And even though the research has disproven the hypothesis — for most of the population — the medical community has been slow to reverse recommendations.  Unless you have medical conditions where your doctor has advised decreasing your cholesterol intake, then eating eggs everyday is just great!

closeup of breakfast egg muffin cups on a white plate

More Favorite Breakfast Recipes

Breakfast Egg Muffin Cups

This Breakfast Egg Muffin Cups Recipe is a delicious make-ahead breakfast packed full of protein, veggies and is totally customizable!
4.49 from 64 votes
Print Pin Rate
Course: Breakfast
Cuisine: American
Keyword: egg muffin cups
Prep Time: 10 minutes
Cook Time: 25 minutes
Total Time: 35 minutes
Servings: 12 egg muffins
Calories: 70kcal

Ingredients

Base

  • 10 large eggs
  • 1/2 cup cottage cheese
  • 1/4 cup milk
  • 1/2 teaspoon salt or to taste
  • 1/4 teaspoon black pepper

Garden Veggie

  • 1/2 cup spinach diced
  • 1/2 cup tomatoes diced
  • 1/2 cup mushrooms diced
  • 1/2 cup cheddar cheese

Meat Lovers

  • 1/2 cup ham diced
  • 1/2 cup bacon cooked and crumbled
  • 1/2 cup sausage cooked and crumbled

French

  • 2 tablespoons green onion
  • 1/2 cup smoked gouda cheese
  • 1/2 cup asparagus diced

Greek

  • 1/2 cup feta cheese
  • 1/2 cup tomatoes diced
  • 1/4 cup kalamata olives diced

Spanish

  • 1/2 cup black beans
  • 1/4 cup green bell peppers diced
  • 1/4 cup tomatoes diced
  • 1/2 cup salsa for topping

Instructions

  • Preheat oven to 350* F. Spray a muffin tin with non-stick spray.
  • Whisk together eggs in a large bowl. Add cottage cheese, milk, salt and pepper.
  • Stir in add-ins for whatever type of egg muffin cup you are making.
  • Pour egg mixture into muffin tin, filling each cup 3/4 of the way full.
  • Bake for about 25 minutes, until the centers are completely set. The edges will slightly brown.
  • Allow to cool for a few minutes before removing and serving. Cool to room temperature before storing.
Tried this recipe?Mention @SuperHealthyKids or tag #SuperHealthyKids!

Nutrition

Serving: 1muffin cup | Calories: 70kcal | Carbohydrates: 1g | Protein: 6g | Fat: 4g | Saturated Fat: 1g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 2g | Trans Fat: 1g | Cholesterol: 157mg | Sodium: 186mg | Potassium: 75mg | Fiber: 1g | Sugar: 1g | Vitamin A: 247IU | Calcium: 37mg | Iron: 1mg

Natalie Monson

I'm a registered dietitian, mom of 4, avid lover of food and strong promoter of healthy habits. Here you will find lots of delicious recipes full of fruits and veggies, tips for getting your kids to eat better and become intuitive eaters and lots of resources for feeding your family.

Learn More about Natalie

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Recipe Rating




132 Comments

I was excited to try out this recipe. It was very easy to make and not time consuming. Unfortunately, they were flavorless and my children gagged. I would have thrown them out but that would’ve been a waste of ingredients, so I ate them. I may make this recipe, but I will have to tweak it with some more flavorful ingredients.

Sorry to heart that Ali. We eat ours with ketchup or salsa. Add salt and pepper to taste. This recipe card doesn’t allow you to put “to taste” on it, so those quantities were probably too small. The good thing about this recipe is that it is versatile so you can pick what veggies you want in there and it will still bake the same. I hope you try it again with the ingredients of your choice. 🙂

We really enjoyed this! I added garlic, onion, and Costco’s 21 seasoning no-salt blend, and also subbed pepper jack cheese for the cheddar for some added kick. For the kiddos, I baked it in mini muffin pans. For the adults, I made it with egg whites, and sprinkled a bit of feta on top. I thought it turned out really well. Thanks!

I took this recipe and added green and red peppers, onions Italian sausage(cooked and grounded) a little garlic salt a dab of butter, salt and pepper. Diced and then put in blender added all the ingredients from your recipe. Including the cheese. Blended lightly. Then put in the cups. They were absolutely yummy. Good for quick on the go. And our company loved them.

Thank you so much for sharing this recipe. It is a great base recipe that I can add in my leftover veggies. I substituted the spinach for kale (because that is what I had on hand) and added onion, garlic powder, and rosemary. They look and taste delicious! Thank you again, I look forward to having a quick and tasty breakfast for my family and I as I start back to work in a week.

Hi! I love this recipe and have tried it several times and every time they come out tasting awful around the edges (where egg and muffin tin touched)….any ideas why this is? It’s almost a fishy taste. Thanks!

Hi ! tried this recipe to encourage my 1 year old baby to eat eggs but after putting it in the oven for 10 min the edges of the muffin started to rise while the center was not !! When they were done they look like little cups any idea why that happened ?
Thank you

I sauteed the bell pepper first, along with small amounts of diced onion and mushrooms–absolutely yummy. Mine cooked well, no sagging middles, no off tastes–perhaps those who complained of such might want to invest in new muffin pans or use paper muffin cups, as sometimes metals react in unpleasant ways. I would also check the my oven temps with an oven thermometer–if baked products fail to respond as expected, oven temp may be an issue

I love making these and freezing them; however, when I microwave them, they are a bit soggy/watery. Any suggestions?
Thanks!

Hi Amiee, I prefer to heat many things from frozen, in the oven (or a toaster oven). I would do this in a 350-375 degree Fahrenheit, preheated oven. I would check them at around 10 minutes. Hope this helps!

Could you make it on a mini muffin tin okay? And if so what do you think the cool time would be?

Absolutely! I would only put 1-2 tablespoons of mixture in each mini muffin cup. And, they will cook quicker as well so be sure to check them after about 10 minutes.

I put black pepper and cilantro with very few spring onion leaves in my version of this instead of spinach. I also sauté the bell peppers and cilantro a little before mixing it in the eggs. It comes off delicious. It’s for me, not my kids. Very delicious and easy to make and have while on the go.

Thank you! My husband is just finding out he’s has Type 2 diabetes. So this recipe would be great for his breakfast. He’s so picky and he’s not allowed any starches.

These egg cups are a life saver. I can’t eat breakfast at home since I take medication and have to wait one hour before I can eat something, so by the time I’m ready to have breakfast, I have to run out of the door for work. Luckily, I have my egg cup, a piece of thin wheat bagel and a cup of blueberries and can eat them at my break at work. My husband and son really like them too. I added cubed turkey breast and for my husand’sand son, I also added some shredded potato. Delicious! Thank you for the recipe

We like these— quick and easy– we have left out bell peppers and spinach and substituted sausage or bacon pieces…. I’ve also added a bit more cheese and a little more salt and pepper. Great for grandkids!
thanks for this basic recipe that can be tweaked to your own.. I’ve shared it with several of my friends for their grandkids!

I just made these for the first time, and also added in some green pepper and red onion So yummy!!!! I think this will be a go-to breakfast for me (also a busy working mom of three kids) and hopefully my kids will love it, too! Thanks for the recipe!

I LOVE these egg cups, and I love your pretty muffin tin! Can you please tell us where you got it/what brand it is? Thank you! 🙂

I used a 1/4-cup measuring cup to fill the muffin tins, and it was the perfect amount. I also used 1-1/2 times everything to fill an entire 12-muffin tin. I’ve found that if I use sharp cheddar it adds more flavor, and I also like nutmeg in my egg dishes.

Very easy. Great for those Sundays when you prep meals for the week…breakfast-check! I’ve also added onion, ham and fresh basil.

Thank you, Amber! You are saving me here. I am new to food prepping and am on a very tight budget. This recipe checks off all the right boxes: it’s healthy, tasty, low cal, and super quick and easy to throw together. I’d love to have more awesome preps for different meals. Thanks again ! Julie Power

This is a SUPER GREAT recipe!! Highly recommend! I did add mushrooms and chorizo sausage ( I had already browned the sausage and crumbled it)… and used half and half instead of milk … but this is so great!! Thank you!

I thought you would like to know that last year I had cancer and while going through the treatment, I made these and kept them in the freezer and on bad days, I would heat one in the microwave and eat it with a piece of toast. For a while, this was the only food I could eat.
I am healthy now but still make these for busy mornings.

I needed something quick but rich and nervously made this for teenagers at a church weekend camp in March. They were a winner and so easy to serve! Doing it again for their teachers this weekend and felt you needed to know how much this works. Thanks for sharing

5 stars
I made these this morning using spinach, broccoli, onions, shredded carrots, mushrooms, and sun dried tomatoes. I placed the veggies in the muffin cup and I cut a piece of my homemade farmers cheese put it on top of the veggies and added the egg mixture, sprinkled some mozzarella on top. What a prize this is, next time I will make a double batch and freeze some (if they last that long!).

5 stars
I make these with chopped broccoli and sautéed red onion.Add any cheese I happen to have, mixed is great. Top with a sprinkle of parmesean.
Yum!

5 stars
This recipe is really yummy! I made them this morning and my whole family ate them with fruit. Super healthy. A breakfast I feel good about. Thanks!

Hi Josh, thanks for reaching out. These egg cups are really all about the egg, so I don’t think you could really get the recipe to work without them.

Hi Nic, Yup! This recipe is flexible when it comes to add-ins, so feel free to try the meats and veggies you like. They’ll keep in the freezer for up to 2 months.

Hi, these are so healthy and practical! Could you please tell me what Cooking spray you use (Coconut oil, olive oil spray??) bc I’ve made them before and the egg has gotten so stuck on the muffin tin that it was virtually impossible to remove completely and I ended up throwing it away. :/ Bought new muffin tins since then but want to take every precaution not to let it happen again since I use my muffin tin all the time for other recipes… but eggs are a tough one! Thanks so much!! 🙂

Hi Susie! I think we originally used ordinary cooking spray (probably vegetable oil) in this recipe. However, I now only use a silicone muffin pan for these egg cups (and for all my grain-based muffins, too.) There’s just no comparison when it comes to ease of use/cleaning and freedom from sticking. The egg muffins pop right out! I’ve tried a few brands of silicone muffin pan and this one is my favorite: https://www.amazon.com/Grazia-G-3002-PREMIUM-Silicone-12-Cup/dp/B00D6V59Y2/ref=cm_cr_arp_d_product_top?ie=UTF8

Such a good method. We alternate ingredients and make a version of these about every two weeks. My 9 year old loves helping to assemble. Sometimes we use semi-cooked zucchini, sometimes we use peppers or onions and ham. Great way to use up left overs!

I made these this morning using asparagus, red onion and orange bell peppers. I used a combo of Swiss and Gouda cheese. I baked them in mini muffin tins and they turned out delicious! I’m a newly diagnosed diabetic so these will be perfect breakfast bites before work.

Hi Nadine, I would start with one minute at a time and then check on them to see if they’re heated through yet. If they seem close but not yet hot, try another 60 or 30 seconds.

5 stars
I had leftover ham from Easter and wanted to make egg cups. Found your recipe, doubled to freeze some, and they are delicious—thank you! ?

5 stars
I love it… And its on our breakfast menu twice a week.. My baby loves it as he is not fond of other spices. Salt pepper and ketchup..
Good luck for next recipe..?

5 stars
A great idea for an easy grab and go breakfast. Perfect for my son who is so fussy at breakfast time but loves eggs. I might even make myself a vegan version using tofu in place of the eggs.

I had leftover ham from Easter and wanted to make egg cups. Found your recipe, doubled to freeze some, and they are delicious—thank you! ?

5 stars
Love these! I’ve made them before and used deli ham and turkey on the bottom for cups. I made another batch today using onions, green pepper, cheddar cheese and chunks of bacon. Added salt and pepper and they were delicious! Definitely love this combo.

Hi! Just wondering how long they keep in the fridge ?
And, for freezer storing, is it better to put them in a plastic container, or a ziplock freezer bag?
Thanks!

They’ll last 3-4 days in the fridge! And you can use either a container or a freezer bag- but I would either wrap them individually, or freeze them on a sheet pan before throwing them together so you can easily remove one at a time. 🙂

4 stars
This recipe is the absolute best! Love how easy and healthy it is… and filling too! Great way to use whatever leftovers you have and throw it all in to make a healthy breakfast!

I was wondering about how to freeze it… how long does it last in the freezer and fridge? TIA?

It’s recommended that you wait until 6 months to introduce eggs to a child’s diet. 🙂 I would make sure to eliminate any choking hazards by mashing or cutting into very small pieces.

I place them on a parchment paper lined baking sheet and freeze just until solid- then I put them all in a large ziplock freezer bag. 🙂

5 stars
Came out great and super easy! Made in silicone jumbo muffin bakeware – spayed w avocado oil and they popped out super easy. 350 for about 30 minutes. Great for meal prep! Used leftover beef short ribs and sweet potato.

4 stars
Im on the noom diet and was getting tired of the “same old”. I tweaked them a bit to fit into my Noom portfolio. No milk used. I used garlic and black pepper seasoning and everything bagel also. I made some with spinach and tomato with pinch of chedder cheese and the others were orange and yellow peppers with sweet onion and the same seasoning as above. I also topped with salsa ! Very good !!

Love this! I’ve made it as is many times and used the base recipe for other iterations. Quick, easy and delicious!

5 stars
Hi Natalie, I can’t wait to make a big batch of these over the weekend to have for breakfast next week! They look so good, and so easy, too. Thank you for sharing this recipe!

Try wrapping them in a paper towel before reheating- that should absorb some of the extra moisture!

5 stars
I just made these for the first time, and also added in some green pepper and red onion So yummy!!!! I think this will be a go-to breakfast for me (also a busy working mom of three kids) and hopefully my kids will love it, too! Thanks for the recipe!

5 stars
Wow! I love the creativity. I am a fan of creating unusual food recipes from simple raw materials. I want to try this for my kids. I’m sure that they love it.

5 stars
How to Store, Freeze, and Reheat Breakfast Egg Muffins. To Store. Let the muffins cool completely, then place them in an airtight container in the refrigerator for up to 3 days. You can store all of the muffins together in a single larger container or portion them into individual containers to take with you on the go.

I modified this recipe to make it my own for my taste. Spinach, celery, onion, red pepper, grape tomatoes, jalapeño and cheddar cheese. Serve with salsa.

5 stars
OMG. These look sooo good. I can’t wait to make them. This is going to be a big hit in our household! Thanks.

5 stars
The only problem I had with these is that I pre-made them for breakfast and most of them were eaten before they were cool enough to put away for the night! (Hey, they were full of veggies, so I’ll take it!)

Thanks for a quick and easy recipe that allowed me to both use up left-overs and give my family something they loved.

I use cottage cheese in mine, and it definitely adds creaminess! I put the eggs, s&p, and other dry seasoning and cottage cheese in the food processor for 30 seconds or so – then mix in more shredded cheese before pouring into cups with veggies and/or breakfast meats. Super delicious.

4 stars
Hi Natalie, This recipe is great but I prefer to cook the spinach beforehand and leave the bell peppers raw before putting it to the egg mixture. When they aren’t cooked thoroughly, they are crunchy, giving texture to the egg cups. Moreover, since my kids love cheese, I added mozzarella plus the cheddar mentioned in the recipe to have a stringy effect when the kids eat it.