Healthy breakfast egg muffins make a delicious savory low carb breakfast or snack on the go! 7 different vegetable-filled flavors to prep ahead and stock your freezer.
NEW: get a free printable with all seven egg muffin recipes here!
I’m so happy to be finally sharing this post with you!
Way back in February I actually started testing these egg muffin recipes, but want to know a little secret? Eggs + morning sickness = no no no NO. So this post was on hold for several months until eggs were tolerable again.
Want to know another secret? I have had a really hard time with egg muffins as a meal prep breakfast/snack for a long time, too. I love them fresh from the oven, but re-heated, I found them squishy and….juicy. I wanted to love them so badly, but it was just a no for me.
But I decided to give them another try, this time adding a little bit of all purpose flour, and some baking powder so they weren’t dense. And I finally found the perfect ratio to give me my perfect, fluffy, protein and veggie-packed egg muffin snack, with no juicy/squishy issues upon re-heating.
Can you make these breakfast egg muffins without the all-purpose flour? Absolutely. If you aren’t turned off by a bit of liquid when you reheat, then by all means, you can absolutely leave out the flour and baking powder. They are lower carb and lower calorie without the flour.
Tips & tools for these breakfast egg muffins:
- make sure you use silicone
or parchment liners, as egg muffins are notorious for sticking to paper liners. You may also have luck with spraying your pan, but sadly, I have not. - I find it easiest to mix my egg muffin batter up in a large glass measuring cup…that way you can scoop/pour using the spout and minimize drips
or 
, as egg muffins are notorious for sticking to paper liners. You may also have luck with spraying your pan, but sadly, I have not.
…that way you can scoop/pour using the spout and minimize dripsHow to prepare these egg muffins ahead:
- store in the fridge for up to 5 days
- freeze for up to 3 months: I would store in a glass storage container like this one for short term (1-2 week) storage and in a large plastic bag like these ones for longer term (up to 3 month) storage.
for short term (1-2 week) storage and in a large plastic bag like 
for longer term (up to 3 month) storage.Base Recipe for Egg Muffins:
This base egg muffin recipe is very flexible:
- omit the flour & baking powder for a lower carb egg muffin
- swap the all purpose flour for gluten free
- add a cup of cooked quinoa for a boost of protein or try this recipe
- these Cottage Cheese Egg Muffins from Closet Cooking are to die for, and another way to add protein to the muffins
1. Sun Dried Tomato, Spinach & Mushroom Egg Muffins
Inspired by these Quinoa Egg Breakfast Muffins from 2015, the combination of spinach, mushrooms and sun dried tomatoes is absolutely delicious! The feta cheese is not necessary but adds delicious flavor to these egg muffins.
2. Kale, Mushroom & Goat Cheese Egg Muffins
These Kale, Mushroom and Feta Breakfast Burritos are one of my all-time favorite breakfast recipes, and I knew I wanted to recreate them in egg muffin form. I thought goat cheese would be interesting to try in egg muffins, and it was! The goat cheese flavor is present but subtle, but if you’d prefer, you can definitely swap for feta cheese. Just remember to omit the salt if you add feta.
3. Roasted Red Pepper & Corn Egg Muffins
If you are craving Southwestern flavors for breakfast, these are perfect for you! The chili powder and cumin give a nice touch of flavor, while the corn and roasted red peppers are ever so slightly sweet. Plus plenty of spinach to sneak in your breakfast.
4. Broccoli Cheddar Egg Muffins
Inspired by these Broccoli Cheddar Breakfast Quesadillas, these broccoli cheddar egg muffins are a great way to sneak some extra broccoli into your diet. Chop it finely so that it cooks through in the oven!
5. Cauliflower Herb Egg Muffins
I’m really starting to come around to cauliflower rice…the perfect way to healthify any meal, including your egg muffins! I just grated my cauliflower on a cheese grater, however you can often find it pre-riced, saving you some prep time. The cauliflower and basil, oregano and dill go perfectly together in these muffins!
Back in the day, I used to work at a pretty awesome bakery/coffee shop, and they also happened to make the most amazing spinach, feta & red pepper quiche. This is 100% inspired by that quiche…and if you like these flavors, you should also check out these Spinach, Feta & Egg Breakfast Quesadillas! So so good.
Watch the video below to see exactly how I prepped my Healthy Breakfast Egg Muffins. It’s so easy! You can find more of my recipe videos on my YouTube channel, or on Facebook.
7 Healthy Breakfast Egg Muffins
Ingredients
base recipe
- 8 eggs
- 1/2 teaspoon salt
- 1/2 teaspoon pepper
- 2 cups mixed vegetables cut into small cubes (ie: zucchini, onion, bell
- peppers torn spinach, mushrooms, broccoli florets)
- 1 cups shredded cheese 1/2 cup reserved for sprinkling muffin tops
- 1/2 cup all purpose flour
- 1/2 teaspoon baking powder
Sun Dried Tomato, Spinach & Mushroom Egg Muffins
- 1/2 cup sun dried tomatoes drained from oil and chopped into small pieces
- 1 1/2 cups chopped spinach
- 1 1/2 cups chopped mushrooms
- 8 eggs
- 1/2 teaspoon salt
- 1/2 teaspoon pepper
- 1 cup shredded cheese
- 1/2 cup all purpose flour
- 1/2 teaspoon baking powder
Kale, Mushroom & Goat Cheese Egg Muffins
- 2 cups chopped kale
- 2 cups chopped mushrooms
- 1/2 cup crumbled goat cheese
- 8 eggs
- 1/2 teaspoon salt
- 1/2 teaspoon pepper
- 1/2 cup all purpose flour
- 1/2 teaspoon baking powder
- 1/2 cup shredded cheese for tops
Roasted Red Pepper & Corn Egg Muffins
- 2/3 cup corn kernels
- 2/3 cup roasted red peppers chopped
- 1 1/2 cups spinach chopped
- 1/2 teaspoon cumin
- 1/2 teaspoon chili powder
- 8 eggs
- 1/2 teaspoon salt
- 1/2 teaspoon pepper
- 1 cup shredded cheese 1/2 cup reserved for sprinkling muffin tops
- 1/2 cup all purpose flour
- 1/2 teaspoon baking powder
Broccoli Cheddar Egg Muffins
- 2 cups broccoli florets chopped small
- 8 eggs
- 1/2 teaspoon salt
- 1/2 teaspoon pepper
- 1 cup shredded cheese 1/2 cup reserved for sprinkling muffin tops
- 1/2 cup all purpose flour
- 1/2 teaspoon baking powder
Cauliflower Herb Egg Muffins
- 2 cups riced cauliflower
- 1/2 teaspoon basil
- 1/2 teaspoon oregano
- 1/4 teaspoon dried dill
- 8 eggs
- 1/2 teaspoon salt
- 1/2 teaspoon pepper
- 1 cup shredded cheese 1/2 cup reserved for sprinkling muffin tops
- 1/2 cup all purpose flour
- 1/2 teaspoon baking powder
Zucchini, Feta & Dill Egg Muffins
- 2 cups shredded zucchini excess liquid squeezed out
- 1/2 cup feta cheese
- 1 teaspoon dried dill
- 8 eggs
- 1/2 teaspoon pepper
- 1/2 cup all purpose flour
- 1/2 teaspoon baking powder
- 1/2 cup shredded cheese for tops
Spinach, Feta & Red Pepper
- 2 cups chopped spinach
- 1 bell pepper finely chopped
- 1/2 cup feta cheese crumbled
- 8 eggs
- 1/2 teaspoon pepper
- 1/2 cup all purpose flour
- 1/2 teaspoon baking powder
- 1/2 cup shredded cheese for tops
Instructions
- Heat oven to 350°F.
- Line a standard sized muffin pan with parchment or silicone liners and set aside.
- In a large bowl, mix together the vegetables, eggs, salt and pepper, until well combined.
- Stir in the flour and baking powder until completely incorporated.
- Spoon the mixture into the muffin pan, filling nearly full. Sprinkle tops with reserved cheese.
- Bake in the pre-heated oven for 20-25 minutes, until muffins are baked through and no longer jiggle.
Notes
Nutrition
Looking for more healthy meal prep breakfast ideas?
- try these 7 Healthy Steel Cut Oats Recipes
- or this No Flipping Meal Prep Protein Pancake
- or these Healthy Freezer Breakfast Sandwiches
Grace
Hi Denise! I am very excited to try these because when I make egg muffins they never quite get the texture I want. I think the flour and baking powder could help that problem. Do you think oat flour would be an okay substitute? I have been trying to cook with it more to consume less gluten/get more nutritional value.
Denise
Hi Grace! I suspect oat flour would work fine, but I have not tried. Can you let me know if you try it? I hope you enjoy them!
Susan
If you are using frozen vegetables i.e. broccoli or riced cauliflower, do you need to cook first or just defrost and drain liquid before adding to recipe? Thank you
Denise
Hi Susan! I wouldn’t bother if they are quite small like riced cauliflower. If you have larger broccoli, I might thaw and cut into smaller pieces.
Mare
Love the sight! New to it! Going to try all the egg muffins but do you know anything about nutritional yeast as substitute for cheese?
Denise
Hi Mare, so sorry for my delayed response. I’ve never used nutritional yeast so unfortunately I’m not much help. Hope you enjoyed!
Traci
Just made these today using your base recipe (omitting the extra 1/2 cup of cheese on top) using red pepper, mushrooms, shredded zucchini and diced ham. Was fabulous! Never used flour in my previous recipes so I’m curious to see if it does cut down on the moisture. That never bothered me but still worth a try! Thanks!
Denise
Love your recipe, Traci! Hope you enjoyed!
Gwen Tatum
My daughter-in-law has celiac and I thought these would be great to make when they visit, but I’m concerned about what flour to uae instead of all purpose. If you are allergic to grains what is the best flour to use? I’m excited to try these. Thanks.
Amy
Gwen, I used coconut flour. I have found that when using coconut flour it tends to absorb more liquid than wheat flour, so experiment a bit. A 1/2 cup of coconut flour was too much for this recipe – mine came out more like a frittata. Still edible, but not quite the texture you’d expect.
Amy
Please note: I don’t have Celiac disease so I don’t know if coconut flour is an acceptable substitute. I would assume so, but check with your daughter. I happened to have coconut flour on hand from another recipe so that’s what I used.
Denise
Hi Gwen! I have used almond flour in these muffins and couldn’t tell a difference. I used the same amount as APF. You can also just leave the flour out 🙂
Kriszta
Hi Denise,
Just discovered your page and found it really useful. Im tottaly new to meal prepping and a bit lost in the overflow of info but love it all so far ?.
I’d like to try out these muffins but have one concerne. Once they are frozen, how to heat them up? Do i need to take them out a day before to defrost in fridge? I usually would eat them at work, so they would travel about an hour before i can heat them. Would that be okay?
Thanks a lot 🙂
Kriszta
Martini
Has anyone tried these using egg whites?
Denise
Hi Martini! Not sure if anyone has tried but I think it would work just fine. I’m not sure how many egg whites you would need, though. Let me know if you try it!
Marlene
Thank You Denise for making ‘breakfast on the go’ so delicious & nutritious! I used 1/4 c. each of whole wheat flour & white flour. Added the 1 c. of cooked quinoa. Both my husband & son raved about the muffins. Freezer friendly as well…it does not get better.
Denise
So happy you enjoyed them Marlene!
Katie
These were great! I tried the kale, mushroom and goat cheese kind. They were pretty simple to put together and I am excited about having an easy breakfast for the rest of the week. I can’t wait to try the other variations. Also, parchment paper liners have changed my life! I’d never heard of them until your recipe and they worked like magic (no sticking whatsoever!) .
Denise
So happy you liked them! And YES I don’t even buy paper liners anymore, parchment liners work on everything, don’t they?!
Cris
These recipes look great, can’t wait to try.
A note, one way to avoid the sticking to the pan that i discovered (without the carb crust) is to line the cupcake tin with prosciutto before pouring in my egg mixture. The last batch of ham and cheese I made slipped right out of the pan.
Denise
I like that idea!
Mary Deane
I love these egg muffins for a quick grab ‘n go breakfast. I usually start with the broccoli cheddar version, and throw in other assorted ingredients that I have on hand like green onions and mushrooms. I use parchment paper cups to bake them, then throw them into a freezer bag once cooled. To reheat, I place the egg muffin on a paper towel to absorb extra liquid and zap in the microwave, which only takes 30 second from a thawed state. Not sure if it’s the flour and/or baking powder, but these baked egg cups are much fluffier and lighter than others I’ve tried. I’ve happily shared this version several times among friends.
Denise
Thank you so much for your detailed review, Mary, I really appreciate it, and I”m so glad you enjoy the muffins!
Supriya Kuttty
Hi Denise, I would Love the look of this bliss, can’t wait to try them at my home. I am in so love with these all. Lovely recipe. Thanks for sharing this recipe with all of us. Looking forward to more recipes like this. Best wishes and Regards.
Denise
Thanks so much, Supriya! Hope you enjoy them 🙂
Jens P
Hi! Super excited to try these! Can you use frozen spinach and what is the equivalent? I am sure I could google this but was curious if you have tried it already? Thanks! Plus I love your site!
Denise
Hi Jens! So glad you like the site 🙂 You can definitely use frozen spinach. I’m not entirely sure what the equivalent would be.
Raquel
Hello!
What are your thoughts on replacing the all-purpose flour with ground flaxseed? Have you experienced some flour changing? Hehe
Denise
Hi Raquel! I’ve never tried ground flax in egg muffins before…I’d love to know how they turn out if you try it though 🙂 GF flour should work if you’re looking for a gluten free alternative.
Jessica
Hi! I tried subbing the flour for ground flaxseed and it did not work! But I subbed the full 1/2 cup that the recipe calls for. I think it would work with a small amount – maybe only a few tablespoons. I’ll let you know if I get a good result!
Denise
Hi Jessica, Thanks for reporting back…ground flaxseed is very different from flour so I’m not surprised. It does work with almond flour if you’re looking for a low carb option?
Sally
What type of shredded cheese are you using please??
Denise
Hi Sally, you can use any cheese, really! I tested these with mozzarella 🙂
Maria Joseph
I love muffins.Recipes you posted is easily understandable and i want to try this muffins.But i don’t eat eggs so what cn i add as an alternative to egg?Please Suggest..
Denise
Hi Maria, unfortunately in these egg muffins, there really isn’t a substitute for eggs. You might want to search for some ‘vegan muffins’ on Google to get egg-free muffins 😀
Dee
Hi Denise,
Love the look of these, can’t wait to try them! One question- what size eggs did you use? Large, x-large? Or grams?
Many thanks 🙂
Denise
Hi Dee! I used large eggs. I think they’re around 52 grams each. Hope this helps!
Dee
Many thanks Denise! ?
Mary
Your combined recipe posts are really helpful and inspiring! Big thanks for the good work!
Denise
So glad you enjoy them Mary!
Erma
Reheat in the microwave?
Denise
Yes! I do 20-30 second increments 😀
Charlie Hogue
This is great! I’ll be making several of these and I also pinned it for many others to see. Thanks!
Denise
I hope you like it, Charlie! Thanks for sharing 🙂