100-Calorie Cheese, Vegetable and Egg Muffins


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Healthy Egg Muffins — Portable baked egg muffin cups that you can enjoy without worry! These healthy egg muffins are stuffed with protein, veggies, and cheese. The best kind of breakfast! Or snack. Or dinner.

100-Calorie Cheese, Vegetable and Egg Muffins

Make-Ahead Egg Muffins Recipe

I thought these egg breakfast muffins would be a good way to sneak in a few extra servings of vegetables and protein for my family. I was right. These muffins are a big hit, and bonus: they’re naturally gluten-free and vegetarian! 

I found myself grabbing one of these egg muffins here and there. And here and there. Before a workout, after a workout, with dinner, for breakfast, in school lunches. We took down the dozen of these in a day.

The egg muffins are soft, yet dense and chewy. I love the texture the vegetables add and I like the surprise of biting into a juicy pea or a crispy pepper piece!

Stack of Healthy Egg Muffins stuffed with veggies and cheese

Ingredients in Healthy Egg Muffins

To make egg muffins in the oven, you’ll need the following ingredients:

  • Shredded carrots
  • Orange bell pepper
  • Frozen peas
  • Frozen corn
  • Eggs
  • Salt and pepper
  • Shredded cheese 

Note: Scroll down to the recipe card section of the post for the ingredients with amounts included and for more complete directions.

Egg muffins with cheese and veggies

How to Make Baked Egg Muffins

These egg muffin cups couldn’t be simpler to prepare! Here are the basic recipe steps:

  1. Liberally spray a non-stick muffin pan with baking spray.
  2. Then, toss together the veggies in a mixing bowl and fill each muffin cup 3/4 full with the mixture.
  3. Crack the eggs into a measuring cup, season with salt and pepper, and whisk with a fork until smooth. Divide the eggs evenly between the 12 muffin cups.
  4. Sprinkle with your shredded cheese of choice, then bake.

Baking Tip

These egg muffins need to bake until the muffins are set, cooked through, and are lightly golden. Note that they will puff in the oven, but sink upon cooling. 

Baked egg muffins out of the oven

Make-Ahead Instructions

Make-ahead egg muffins are the perfect way to meal prep for the week ahead!

You can make a whole batch of these in advance and keep them for up to about a week in the fridge and then just reheat them in the microwave for 15 to 30 seconds. Makes a quick on-the-go snack!

However, I actually like them cold. (But I also love cold pizza, so do what sounds good to you.)

If you want to freeze the egg muffins, I recommend letting them cool completely to room temperature before flash freezing on a parchment paper-lined baking tray. The muffins should harden within 1 hour and can then be sealed in a freezer bag without fear of them getting squished or sticking together.

For best results, reheat egg muffins from frozen. If you thaw them first, the vegetables will weep and the eggs will become soggy. No, thank you!

Healthy egg muffins refrigerate for a quick snack

Recipe FAQs

Can I Add Other Veggies to These Egg Muffins?

Definitely! I used shredded carrots, orange peppers, frozen peas and corn, but you can use almost any veggie you like. It’s the perfect produce drawer clean-out recipe.

Rather than the shredded carrots, which serve to really bulk up the vegetable mixture, you could grate or dice leftover potatoes or sweet potatoes. Or work in some broccoli, asparagus, spinach, kale — whatever is seasonal or lurking in the bottom of your produce drawer and needs to get used, stat.

Can I add bacon, ham, or sausage to the muffins?

Yes, but you MUST cook bacon and sausage in a skillet before adding to the muffin cups. The egg muffins aren’t baked for long enough to cook raw bacon and sausage, plus all the veggies and egg.

Can I Use Egg Whites or Liquid Egg Replacer?

I’ve only made these baked egg muffins with whole eggs, although you could likely use liquid eggs or just whites. If you use one of these egg alternatives and this recipe turns out well for you, please let me know in a comment below! 

Can I Make Mini Egg Muffins? 

I used a regular muffin pan to make this egg muffin recipe, but you’re welcome to make mini egg muffins if desired. Just note that the bake time will be significantly reduced. 

Why are my egg muffins soggy?

Baked egg muffins can turn out soggy if too much liquid is added to them, or if the vegetables release a lot of liquid. To keep this recipe super simple, I didn’t saute the vegetables for this recipe (which a lot of egg muffin recipes have you do). However, I also didn’t add any liquid, such as milk, to the egg mixture. So, you shouldn’t have any issues with soggy egg muffins if you follow my recipe as written!

Can I Freeze Egg Muffins? 

Yes! This recipe is fabulous as make-ahead egg muffins. Flash freeze on a parchment paper-lined baking tray until firm, then seal in a freezer bag and reheat (from frozen!) in the microwave for about 30 seconds. 

Baked egg muffins for anytime

Tips for Making Healthy Egg Muffins

Non-stick spray: When making these egg bake muffins, you MUST spray the heck out of your muffin pan with non-stick spray. Then, run your finger through the spray and around the sides of the cups because every inch must be liberally coated with spray. If you miss a spot, you’ll be chiseling off stuck food with a knife. I speak from lots of experience.

Carrots: If using shredded carrots in this baked egg muffins recipe, I highly recommend shredding the carrots yourself as opposed to buying bagged shredded carrots. I find bagged shredded carrots to be too big, coarse, and tough due to the preservatives added.

Cheese: I topped the muffins with shredded mozzarella for extra flavor, richness, and it helps the muffins brown nicely on top. Use your favorite cheese. Or, if you’re trying to be good, omit it.

Recipe Video Tutorial

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4.51 from 51 votes

100-Calorie Cheese, Vegetable and Egg Muffins

By Averie Sunshine
100-calorie, portable, baked egg muffins that you can enjoy without worry! These healthy egg muffins are stuffed with protein, veggies, and cheese. The best kind of breakfast! Or snack. Or dinner.
Prep Time: 15 minutes
Cook Time: 20 minutes
Total Time: 35 minutes
Servings: 12
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  • 1 ½ cups shredded carrots, from about 4 medium peeled and trimmed carrots*
  • ½ cup small diced orange bell peppers
  • ½ cup frozen peas, I didn’t thaw
  • ½ cup frozen corn, I didn’t thaw
  • 8 large eggs
  • salt and pepper, to taste
  • 12 tablespoons shredded cheese, divided (I used Mozzarella)


  • Preheat oven to 375F. Spray a Non-Stick 12-Cup Regular Muffin Pan extremely well with cooking spray. Spray the base of the cavities and sides, then run your finger over the sides so that every inch is liberally coated with spray or you will be chiseling off stuck food; set pan aside.
  • In a large bowl add carrots, peppers, peas, corn (or mix and match with your favorite vegetables; read blog post for suggestions) and toss to combine.
  • Loosely pile about 3 tablespoons of vegetable mixture to each muffin cavity, or enough so that each is filled to about 2/3 to 3/4 full; equally distribute filling mixture among cavities until gone; set pan aside.
  • In a 2-cup glass measuring cup (the measuring cup makes for easy pouring), crack the eggs and lightly beat with a whisk.
  • Add the salt and pepper, to taste, and whisk to combine.
  • Pour about 2-3 tablespoons of egg into each cavity, equally distributing among the cavities. They will be about 3/4 full after being topped off with egg.
  • Top each cup with a generous pinch of cheese, about 1 tablespoon each.
  • Bake for about 18 to 20 minutes, or until muffins are set, cooked through, and are lightly golden. They will puff in the oven, but sink upon cooling.
  • Allow muffins to cool in pan on top of a wire rack for about 10 minutes before removing. You will likely need to rim each cavity with a small knife to help dislodge muffins. I find it easiest to rim with a knife and then ‘pop’ the muffin out using a small spoon.


  • *I recommend shredding the carrots yourself as opposed to buying bagged shredded carrots which I find to be too big, coarse, and tough due to the preservatives added.
  • Muffins will keep airtight for up to 1 week in the fridge; reheat gently in the microwave or serve cold.


Serving: 1, Calories: 100kcal, Carbohydrates: 6g, Protein: 7g, Fat: 6g, Saturated Fat: 2g, Polyunsaturated Fat: 3g, Cholesterol: 131mg, Sodium: 133mg, Fiber: 1g, Sugar: 2g

Nutrition information is automatically calculated, so should only be used as an approximation.

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Asparagus, Peas, and Smoked Gouda Frittata — Even the pickiest eaters will eat green vegetables in this healthy & easy 25 minute recipe!

Asparagus, Peas, and Smoked Gouda Frittata - Even the pickiest eaters will eat green vegetables in this healthy & easy 25 minute recipe!

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White Cheddar and Dijon Baked Eggs - Fast & easy comfort food that's ready in 15 minutes! The Dijon & cheese just jazz these eggs right up!

Kale and Tomato Frittata — This frittata is healthy and I love the texture contrast between the tender eggs, chewy kale, and juicy tomatoes in this frittata.

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Welcome to AverieCooks! Here you’ll find fast and easy recipes that taste amazing and are geared for real life. Nothing fussy or complicated, just awesome tasting dishes everyone loves!

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Please note: I have only made the recipe as written, and cannot give advice or predict what will happen if you change something. If you have a question regarding changing, altering, or making substitutions to the recipe, please check out the FAQ page for more info.

Recipe Rating


  1. 5 stars
    I did this with egg whites and bacon and one batch with sausage. you don’t really even need to spray with oil with the greasy meats in there.

  2. 5 stars
    I did this with egg whites and bacon and one batch with sausage. you don’t really even need to spray with oil with the greasy meats in there.

    1. Thanks for the 5 star review and glad that the work well for you. I do recommend spaying the tin if someone isn’t using greasier meats and/or doesn’t fully trust their muffin pan. Sometimes they do stick and with egg…it can be like cement if it does!

  3. 5 stars
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  4. The review link is useless in a printout. I doubt you’re leaving that in there to please your readers. Most of the chatter at the top doesn’t warrant a second read and isn’t useful for folks who are saving recipes to use again and again. If I have to cut, paste, and reformat a recipe prior to printing I’ll stick with cooking websites that are more convenient and ones that give more thought to the environment. There’s really no good reason why you can’t format most recipes to print on a single page.

    I understand completely if you’re just replying from a customer service role that can’t really help with such issues.

  5. Any way to work with your website team to remove the long paragraph at the top and the “reviews” link out when we click to print? Many of your recipes would fit on one page without that big waste of space, and paper.

    1. It’s hard to please everyone with regard to printing things out. You could just copy/paste the part you want in an email to yourself and print that only.

  6. 5 stars
    What a great idea! I used leftover sauteed veggies that added some nice flavor. Instead of cooking spray I used coconut oil and had no issue with sticking to the pan.

    1. It’s an automated program so it’s not always perfectly accurate and things can vary.

      I calculate about 50 calories of egg, 20 calories of vegetables, and 20 calories of cheese per muffin just using common sense. Of course I always recommend people to do their own calculations if nutrition info is very important to them.

  7. I used well greased custard dishes. Worked slick.
    Any leftovers can be used up easily making these.
    Quick, adaptable yummu

  8. I just tried the cheese, veggie and egg muffins. Your directions were perfect, they turned out great!  I like that the veggie ingredients can be flexible. Taking the whole batch to work with me. – breakfast for a week!   So simple. Thanks so much for sharing. 

    1. Thanks for trying the recipe and I’m glad it came out great for you! And yes flexible ingredients and glad you have breakfast for the week!

  9. Do you just store these in the fridge? And when you ate them, did you just eat them cold? Or did you zap in the microwave?

  10. I see that Lily made them using mini muffin tins. I would like to do the same but how long should they take to bake?

    1. Thank you! I was trying to read other comments, but there were too many to scroll through on my phone! Can’t wait to try them as they seem perfect for a lady who is always late: me!

  11. These were awesome and even my picky kids loved them!

    I used silicone muffin liners so the muffins popped out no problem without the need for grease.


    1. Thanks for trying the recipe and I’m glad it came out great for you! Glad the silicone liners worked liked a charm and that picky kids approved!

    2. Where did you get your silicone muffin liners?  I live in Canada and would love to get some. I have a 6 cup silicone muffin “pan” and made these, adding just a bit of cooked quinoa and grated zucchini to keep them moist.  Amazing!  

      1. Thanks for trying the recipe and I’m glad it came out great for you with the quinoa and zucchini. I would just google or do an amazon search of what you can get with delivery options to Canada and I’m sure you’ll find something easily.

  12. Warning: do not use cupcake papers! 
    These are delicious. I read through some comments, mostly about how they stick, and thought Well, silly people, just use cupcake papers! Ha! bad idea. They do, indeed, shrink up immediately when you pull them out of the oven, and if they are in papers? They shrink in every direction! They still tasted great, but the paper thing was a BAD IDEA! 

    I used bacon pieces, kale, onion and cheddar. Yummy! 

  13. I’ve got these in the oven right now! Smells like breakfast. It’s only two of us, so I’m looking forward to throwing these in our lunchboxes for the week or having them for a quick breakfast.

    I used some diced onion, corn, carrots, and some bacon crumbles (freshly cooked, not the “bits”)–didn’t have peas, but I think they’ll still come out great. I also added about two tablespoons of salsa to the beaten egg mixture. I think it will pair well with the corn and monterey jack I used.

    I’m so excited to be making these! They’ve been on my “to bake” list for a while. Thanks for the recipe!

    1. I would say let them come up to room temp on their own and then zap them in the micro just until warmed, maybe 30 seconds.

  14. Awesome recipe! I added some different fillings and it turned out great! I sautéed onions, mushrooms, and spinach then mixed them all together with cut-up pieces of sausage. Not vegetarian of course but the textures worked out really well with each other. Oh and I also made them in a mini muffin pan so they came out cute and bite-sized! 

    1. Thanks for trying the recipe and I’m glad it came out great for you! Love the add ins you used and that you made them mini, so cute!

  15. Using non-stick spray on some non-stick pans can actually gunk them up.  I like the coconut oil idea or maybe butter or olive oil.  Also, if you put baking soda on your pans with some warm/hot water (too much dilutes the baking soda) it will soften the stuck-on food and make it easier to wash off.

  16. This recipe looks delicious and creative. This is a new way to have eggs at breakfast. The process seems easy to follow. I will try this soon! 

  17. your egg muffin recipe looks easy and delicious, I’m going to try mine Abby adding some low fat ricotta to my eggs instead of the cheese on top, adds flavour to the recipe,  I use it in scrambled eggs every time. Enjoy

  18. I noticed that you remarked on greasing the muffin tray very well and though I would share my experience with you for what it is worth. I have the same experience as you with the sticking but loved the idea of the muffins. So this time when making yours, I put baking paper into each cup. I cut it into squares to fit then squished it and fitted it into the holes. I put my mixture in and baked them as you directed. No sticking and BTW these are awesome. Thank you for sharing.

  19. I absolutely loved these!! :) Though I had to make some adjustments since I was sort on some ingredients it was still tasty!! I added onion and a little garlic to the veggies and paprika and almond milk with the eggs for I only had 6. Yummy yummy yummy and my family ate them all in one go :P

    1. Thanks for trying the recipe and I’m glad it came out great for you! The garlic, almond milk, and paprika all sound like perfect touches and that your family ate them all in one go! Love it!

    1. You can try it; not sure if eggs will stick to them or not. My guess is yes, but I haven’t tried.

  20. We make thrm with mini muffin cases. Make 12 in a morning and myself, 3yr old and one year old polish them off for brekkie. I always plan on leaving some for snacks throughout the day but NEVER happens

  21. Love these!!! My add ins were grated carrot, zucchini and spinach. Paired with 1/2 cup steel cut oatmeal and few blueberries equaled perfect breakfast. Very filling and satisfying. Looking forward to trying more of your recipes!!!!

  22. Hi there:

    Great recipe! Just wanted to add that I use the individual silicone muffin cups…no need for oiling and the muffins literally fall out!

    1. I would say 5 days or so and I reheat in the micro and I also eat them cold…I love cold pizza though. And something about these kind of reminds me of that!

  23. Quick question…do these freeze well? I am pregnant and trying to come up with easy meal ideas that I can make in advance and freeze so that after the baby comes I won’t have to do a lot of cooking! These look amazing!

    1. I have frozen them and I am fine with the texture after thawing. It changes a bit but I honestly don’t care. If I was pregnant and it was this and pre-making things to have on hand or not, I would DEFINITELY do it. You will thank your lucky stars for every meal you have stockpiled. I was hungrier the first 6 mos of nursing than I ever was pregnant. Stockpile!! :)

  24. I just made these using the last of a bag of frozen veggies I had in the freezer and the last of a bag of shredded Gouda I had in the fridge. I used 6 eggs and made 9 muffins because I was a little low on veggies. They were delicious! I love that this is easy and fool proof and can be made using the remnants of whatever I have in the house. This has shot the top of my healthy weekday morning breakfast list.

    1. Thanks for trying it and glad it was a hit! And I totally agree that this is a great ‘remnant’ recipe – can use up WHATEVER you have on hand! Glad it’s shot to the top of your healthy weekday breakfast list!

  25. These were great! I’ve tried making egg muffins a couple other times and they did not come out well. So glad I tried your recipe! I love how detailed you are with your instructions. :)

  26. I dont know if my muffin pan just has larger wells than yours, but it took me 11 eggs instead of eight. So a fair warning to those with larger welled pans, you’re gonna need a couple more eggs than the recipe calls for, which will also make it more than 100 calories.

    1. I linked to the pan that I have. Also you could add more veggies and beef those up, meaning you’ll still need the same amt of eggs if there’s slightly more veggies in every cup – and they would only very nominally increase the cals.

  27. My teenaged daughter is getting interested in nutrition and cooking. She found your blog and we made the egg muffins breakfast this morning. We used six eggs and a six hole muffin tin. I pre-cooked some spinach in the microwave and snipped it up, added sweet potatoes (had some leftover roasted cubes), shredded carrots and peas, yum-yum. Thanks for the recipe.

  28. Seriously girl, I love how bright and cheery your photos are! They always make me smile… And drool! ;) Love these delish little egg muffins. Pinned, as usual!!

    1. These were the eggs I had told you about right when you posted yours. I had already made there like the day before :) Thanks for the pin!!

  29. These little bites are adorable Averie! Such a perfect on the go breakfast and I love that they are only 100 calories -that means I can have more – pinning:)

  30. Averie, I’ve been drooling over these every time I see them on Pinterest! Pinned to my must make board!!!

    1. Thanks for noticing them on Pinterest and for repinning :) Ive been seeing your browned butte cookies the past few days and repinned!

  31. the lovely golden color made these irestible so i made a half dozen with edamame filling in for peas plus baby spinach / they are somewhat too “eggy” for me so next time a little flour to hold them together and a lot less egg / thanks for a good idea

    1. Well yes there’s 8 eggs in the recipe so they’re pretty eggy…haha :) But tweak things as you see fit so they taste just the way you want them! I think also the peppers that I used cut a lot of that eggy taste since they’ve got a fairly dominant flavor so maybe try those next time, too!

  32. love the yummy cheese you add to yours! I do this for my husband every week. I make this exact same ones but with chicken flavored rice and spinach. He loves them and eats them on his way to work. He says they keep him full all morning long!

    1. And I totally believe him! They’re so satisfying and glad you have your own version!

  33. I need things like this in my life for breakfast, I get stuck on the same oatmeal, whole wheat waffle or greek yogurt routine this would be an awesome change. But I could not omit the cheese, HELL NO! lol

    1. And it’s way too easy to get into other ‘ruts’ too – like grabbing cookies for breakfast. Not that I would know :)

  34. I love cold pizza too! I used to eat it for a lazy breakfast on the weekends after a late night out with friends on Fridays. Something about the flavors being even better the next day… Those leftovers never lasted long in our fridge! With veggies, I tend to forget about the half-serving here, or two baby carrots there, and end up randomly cutting them all up and tossing in a salad. Love the idea of egg cups instead, especially since they’re more portable and practically finger-food!

  35. These would be perfect for making in large batches and freezing for hubby morning brekkies!

  36. Wow, sweet. The recipe was not what I was expecting. I love surprises.
    I love the cheerful color too. Breakfast would start off with a sunny start.
    The low calories and not losing any taste is quite positive—OF COURSE.

  37. These are so cute Averie! Love that they are only 100 calories and a perfect on the go breakfast! Pinning!

  38. love these! I just made something similar but i Love your version! Happy Cinco De Mayo

  39. I’ve made very similar recipes before. Little egg cups like this are awesome to have in the refrigerator for a quick breakfast. Love the idea to add carrots or potatoes!

  40. I love that these are portioned out so you can grab and go. What a great way to use up leftovers and for less than 100 calories it’s a win win. Can’t way to try.

  41. These are the perfect breakfast on the go! Love how portable they are–yumm!

  42. The egg muffins looks delicious and perfect to pack for when you’re on the go in the morning!

  43. So that’s the secret? I’ve given up on egg muffins because I can’t deal with them sticking. In fact, I froze a bunch a while ago and just tossed them out because they reheated like crap and just got completely crumbled up all to hell.

    These look great though, and with garden season upon us….YES!

    1. I know people do freeze these but honestly one batch doesn’t really make enough to freeze for us at least because they last up to a week in the fridge and they’re small and really good! and honestly no way they’d last a week anyway. Point being, I’d just stick with the fridge if at all possible rather than the freezer. That could have been the culprit in part!

  44. This is a great recipe – perfect for my husband right now too. He’s on that clean eating 30 day thing. (It’s annoying. ;) )

    1. Well I give him props for doing it in the Crazy for Crust house with all those goodies laying around :)

  45. I love these little things!! My favorite add ins are spinach and bell pepper. I bake them in ramekins and eat them topped with salsa. I haven’t made them in a while so thanks for the inspiration!

    1. I almost added spinach to these and then got sidetracked and forgot! But that was in my original plan to use it…oh well, next time :) Topped with salsa would be so good!

  46. Averie, I could see myself grabbing a few or more of these through out the day, too… they look amazing!

  47. I have been wanting to make egg muffins for sometime now!! Can NOT WAIT to make these!!! Breakfast tomorrow!

      1. Have you tried making them in muffin cases? Just wondered if that might be simpler than pan cleaning?!

  48. Waaaaaaant!! I’ll take all 12 and call it a day! Seriously, I can totally see myself inhaling the batch in one day. They sound amazing!!

  49. These look delicious! I have no doubt they’d be gone in the blink of an eye as my menagerie loves eggs. :)

  50. I think I would skip the veggies on a few, as, while my kids like them, they don’t like their food “mixed” (and I would completely leave out all peas!). I really like this idea. I hate cooking a hot breakfast on busy school mornings so unless we are reheating pancakes or I make crockpot oatmeal, it’s typically cold cereal for breakfast here. But this would be tasty and make me look like a more ambitious mom than I really am …

    1. You could make these on Sunday night and depending on how many kids/appetites there are, you could dole them out…til Friday. LOL That’s what I did last week for my daughter…1 for breakfast with some fruit, and 1 in her lunch box with other stuff of course. But M-F was handled…breakfasts and lunches. Soooo handy!

  51. These are my kind of breakfast – they look so good and only 100 calories means I can eat at least 3!

    1. Exactly! Since we’re baking and taste-testing nonstop, you’ve gotta save cals where you can :)

  52. Averie, these look so cute and delicious! I love foods that you can just grab ‘n go, and these look like the perfect breakfast muffin to do so!

  53. Oh man, I can definitely see how these got eaten in a day.I love recipes like this too! Plus, there are so many fun variations to make once you have the base. Love this!