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One batch of this egg muffins recipe and you’ll never want to live without them in your fridge again! Sometimes called breakfast egg muffins, egg muffin cups or mini frittatas, they make a great meal prep low carb breakfast for busy days — whether your rushing out the door or rushing to get to your computer like me. Pair them with some bulletproof coffee for a filling, protein-packed morning meal.
This easy egg muffin recipe is made in a muffin tin with veggies, eggs, milk of choice, and cheese. I also have 15 variations and a rule of thumb for the ratios below, so you can customize it to your heart’s content.
If you prefer the yolks and whites separate, try oven baked eggs (also made in a muffin tin!) or cloud eggs instead.
Why You’ll Love This Egg Muffin Cups Recipe

Ingredients & Substitutions
This section explains how to choose the best ingredients for egg muffin recipes, what each one does in the recipe, and substitution options. For measurements, see the recipe card below.
- Vegetables – I used broccoli, cauliflower, and bell peppers. Make it your own by choosing your favorite low carb vegetables, or simply use what you have in your fridge right now! Notes on the veggies:
- Fresh or frozen: You can use fresh or frozen vegetables — both will work great — but either way they do have to be cooked before adding to the egg mixture.
- Cooking method: I prefer to use roasted vegetables because it imparts so much flavor, but any cooking method (steaming, boiling, or sauteing in a skillet) will also work. Be sure to pat dry if steaming or boiling.
- Pre-cook: Pre-cooking the veggies is important to ensure that your breakfast egg muffins don’t end up soggy and watery.
- Aromatics – Not required, but I love adding some minced garlic. Caramelized onions would also be a delicious addition. For convenience, you could just whisk in 1/2 to 1 teaspoon of garlic powder or onion powder directly into the egg mixture.
- Olive Oil – For roasting the vegetables. Avocado oil works great, too.
- Meat – I didn’t add any to the basic egg muffin recipe below, but you can also add some cooked crumbled sausage, ham, or bacon. Be sure any meat you add is already cooked, because it will not cook through if you add it raw.
- Eggs – I prefer to use whole eggs, but egg whites would also work if you want egg white muffins. To do this, replace each large egg with 3-4 tablespoons of egg whites (about 1.5 egg whites).
- Milk Or Cream – Helps the eggs get fluffy! This egg muffin cups recipe is written using heavy cream, but you can swap it for the milk of your choice. Regular dairy milk or half & half will work but will increase carb count. You can also use coconut milk or almond milk for dairy-free options.
- Cheese – I used shredded cheddar, but you can also try mozzarella, gruyere, feta, or any other cheese you like. Get the full cheese list here for ideas. For a dairy-free option, simply omit the cheese (and use almond or coconut milk above).
- Sea Salt & Black Pepper

How To Make Egg Muffin Cups
This section shows how to make egg muffins in the oven, with step-by-step photos and details about the technique, to help you visualize it. For full instructions, including amounts and temperatures, see the recipe card below.
- Cook add-ins. Toss the broccoli, cauliflower, red pepper, and garlic (or any other vegetables you are using) with the olive oil. Spread out in a single layer on a baking sheet and roast until edges are browned. If you are making your egg muffins with bacon, sausage, or other meats, pre-cook these as well.
- Portion. Line a muffin pan with parchment paper liners or silicone cups. (You can also just spray with cooking spray, but liners make the muffins easier to remove and more portable, and require less cleanup.) Divide roasted vegetables among the cups.


- Whisk egg base. Whisk together the eggs, heavy cream (or milk of choice), sea salt, and black pepper. Stir in cheese of your choice. Pour the mixture into the egg muffin cups.
- Bake. They are ready when the eggs are set. Enjoy this easy breakfast recipe right away, or see storage instructions below to store for later.


How Long To Cook Egg Muffins?
With already pre-cooked meats or vegetables, bake egg muffins for 15-20 minutes.

FYI: It’s common for egg muffin recipes like this one to deflate a bit.
When they are baked, the air bubbles in the egg expand, and they deflate as they cool. One way to reduce this effect is to let the muffins cool more slowly, so keep them in the pan to cool before removing them. This will help, but know that it’s totally normal for egg muffins to collapse a little.

15 Flavor Variations
One of the best things about this egg muffin cups recipe is that it’s so versatile and easy to customize to your taste. Try these combinations for add-ins:
- Ham & Cheese – Diced ham and chopped American (or cheddar) cheese.
- Bacon Cheddar – Classic cooked bacon and shredded cheddar (but really, almost any cheese goes with bacon!).
- Mushroom Swiss – Sauteed mushrooms and shredded Swiss cheese.
- Asparagus Gruyere – Chopped cooked asparagus (a great way to use up leftover roasted asparagus!) and shredded Gruyere cheese.
- Spinach Feta – Spinach and crumbled feta cheese. Spinach is very watery, so for spinach egg muffins, use either fresh sauteed spinach or frozen spinach drained well.
- Garden Veggie – Bell peppers, mushrooms, onions, and chopped tomatoes (pat very dry and omit seedy parts). Cook the mushrooms and peppers, but not the tomatoes.
- Greek – Cooked bell peppers and red onions, sliced olives, fresh basil, and crumbled feta cheese.
- Pizza – Chopped pepperoni and shredded mozzarella. Dip in marinara sauce for serving.
- Tex-Mex – Cooked chorizo, sauteed or roasted bell peppers, and choose from pepper jack, Cotija, or Mexican blend cheese.
- Jalapeno Popper – Cooked bacon, chopped jalapeno peppers, sliced green onions, shredded cheddar, and small pieces of cream cheese. You only have to pre-cook the bacon (try oven bacon or air fryer bacon as hands-off methods) for this one.
- Meat Lover’s – Sausage, pepperoni, Canadian bacon, and either cheddar or mozzarella (or both!). You can also keep it simple with sausage egg muffins only.
- Sun-Dried Tomato & Zucchini – Sauteed zucchini, sun-dried tomatoes, and goat cheese. You’ll need to cook down the zucchini a lot, otherwise it has a tendency to get watery.
- Garlic Parmesan – Sauteed minced garlic, Italian seasoning (or fresh herbs like pasley and chives), and shredded parmesan cheese. This version is missing bulky add-ins, so add 3-4 more eggs and an extra tablespoon or two of milk/cream to make up for it.
- Dairy Free – Omit the cheese (replace with 1/2 cup of other add-ins) and use full-fat coconut milk (or almond milk, but coconut milk makes for a richer result) instead of heavy cream.
- No Carb Egg Muffins – To keep carbs super low (less than 0.5g per serving), don’t include any veggies. Any combination of eggs, cream, meat, and cheeses is fine. (You can even include them on an egg fast if you make them with just eggs and cheese.)

RULE OF THUMB: The basic ratio for 12 egg muffins is 8 eggs, 1/4 cup milk of choice, 3/4 cup cheese, and 2-2.5 cups of add-ins.
The volume for the add-ins is after cooking, so you’ll start with more (about 3 cups of most vegetables will make 2-2.5 cups cooked).
Storage Instructions
- Store: Keep egg muffin cups in an airtight container in the refrigerator for up to 5 days.
- Meal prep: These are awesome for meal prep, so you can definitely make a batch ahead for quick breakfasts or snacks! Alternatively, you can cook the add-ins (vegetables and/or meats) ahead of time and bake them fresh.
- Reheat: Warm up your breakfast egg muffins in the microwave for about 30 seconds, or in the oven at 350 degrees F, until warm. Be careful not to overcook, or they will be rubbery.
Can You Freeze Egg Muffins?
Yes, you can freeze egg muffins. Let them cool completely at room temperature, then freeze in a freezer bag for 2-3 months. Thaw them in the fridge overnight before reheating.
More Healthy Low Carb Egg Recipes
If you like this breakfast egg muffin recipe, you might also like some of these other egg recipes:
Tools To Make Egg Muffin Cups
- 3-Compartment Glass Meal Prep Containers – Pop a few egg muffins in here with a side of green salad and some nuts, and you’ve got a nutritious breakfast that’s quicker than the drive-thru.
- Muffin Tin – This egg muffin recipe is written for a regular-sized muffin tin (this one is my favorite), but you can easily use a small muffin tin. You’ll get about twice as many muffins and the cook time will be much faster.
- Muffin Liners – A must for easy cleanup! You can use silicone muffin liners or parchment paper liners.
Breakfast Egg Muffin Cups Recipe
Egg Muffin Cups
Choose from 15 flavors of this breakfast egg muffin cups recipe with veggies, eggs and cheese! It's healthy, low carb, and easy to meal prep.
Recipe Video
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Ingredients
Tap underlined ingredients to see where to get them. Please turn Safari reader mode OFF to view ingredients.
Instructions
Tap on the times in the instructions below to start a kitchen timer while you cook.
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Preheat the oven to 400 degrees F (204 degrees C). Line a baking sheet with parchment paper or foil (grease if using foil).
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In a large bowl, toss together the broccoli, cauliflower, red pepper, minced garlic, and olive oil.
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Arrange the vegetables in a single layer on the baking sheet. Roast in the preheated oven for 15-20 minutes, until the edges of the broccoli are browned.
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Meanwhile, line a muffin tin with 12 parchment muffin liners or silicone muffin liners.
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When the vegetables are done, keep the oven on. Arrange the veggies evenly in the muffin cups.
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Whisk together the eggs, heavy cream, sea salt, and black pepper. Stir in the cheddar cheese. Pour the egg mixture into the muffin cups over the vegetables.
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Bake for 15-20 minutes, until the eggs are set.
Last Step: Leave A Rating!
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Recipe Notes
Serving size: 1 egg muffin
For other flavor options, see the blog post above.
Nutrition facts are provided as a courtesy. Have questions about calculations or why you got a different result? Please see our nutrition policy.
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72 Comments
Dana
0These are perfect for busy mornings! My kids really love the bacon and cheddar version, I love any of the veggie versions. What a life saver when we’re rushing to get out of the house.
Cam
0This was so easy to make and tasted super delicious! Love this!
Lisa
0We really love this one. It’s so easy to take it on the road with you. I’ve tried different variations and they are all delicious.
Debbie
0Easy to make , and very yummy !! I read comments below and saw what others added.. I will do bacon and cherry tomatoes next time !! Does it matter what kind of bacon you use??
Wholesome Yum D
0Hi Debbie, Any kind of bacon you prefer will work.
Amaya
0Delicious! Perfect recipe turns out amazing every time. I’ve been making this every day for breakfast for the family!
shauna
0Hi Maya, your recipes are listed as dairy free, however you have given no dairy free options that work well with your recipes, Dairy free milk can be extremely thick like coconut cream or extremely thin as in Silk milk. Some of these options are great when baked others can completely ruin a recipe. The same is true for cheese substitutes, some are like cream cheese others can be hard like brick cheese. A few are bakeable but often the cheese substitutes do not melt or bake well. To list your recipes as dairy free you really need to give us the dairy free options that have worked for you in these recipes. I would love to see your successful dairy free options included in your recipes. It will help those of us with severe dairy allergies to succeed in building the yummy recipes you have created, thanks and I look forward to seeing your workable dairy free suggestions!
Maya | Wholesome Yum
0Hi Shauna, Not all my recipes are dairy-free. For this recipe to be dairy-free, it states to omit the cheese (replace with more veggies) and use a plant-based milk instead of the cream. Here are all the recipes with a dairy-free option (or are naturally dairy-free). For ones in this category that have dairy, I include instructions to substitute either in the post or on the recipe card.
Sandra
0Where are your recipes for sandwiches not using bread? Using, lettuce or cucumber for example. I saw them yesterday but can’t find them now.
Wholesome Yum D
0Hi Sandra, Here is my recipe for a cucumber sub and a bell pepper sandwich.
Tori
0I know I’m going to have a good week when I prepare these on a Sunday. Love to use frozen spinach (that I wouldn’t eat otherwise) as the base and pour either sausage or bacon and egg filling on top! I usually pair it with avocado and a piece of low-carb toast. Fool-proof recipe.
JESUS
0Hi–these look great! I’m not a baker so apologize if this is not clear, but I’m seeing a lot of muffin tins with six cups. Wondering if the one you use with 12 is “mini” or standard size, and then whether the six cup ones are jumbo or the same size (e.g., meaning I’ll need to halve the recipe or use two six cup ones), if you know.
I just ordered the set below and then realized it’s only six cups; imagine if using a six cup jumbo model, I’ll have to cook longer and possibly modify the recipe, so want to make sure I’m using the right one. Any idea?
Thank you for all the awesome recipes!
https://www.amazon.com/gp/product/B01N90FWOG/
Thanks.
Wholesome Yum D
0Hi, A muffin tin with 12 cups would be the standard. Yes, you would have to adjust the cooking time because a 6 cup tin would be jumbo muffin.
Teresa Locklear
0I’m sure I saw a recipe for cream cheese blueberry muffins on your page, but can’t find it now. Can you please tell me how to get to it…. p.a. love your recipes……thanks
Wholesome Yum D
0Hi Teresa, I don’t have a recipe for blueberry cheesecake muffins, but I do have a regular blueberry muffin with almond flour recipe.
Maya | Wholesome Yum
0Hi Jesus, The link you posted goes to a set that includes a 12-cup muffin tin. But to answer your question, this recipe uses a muffin pan with standard sized cups (not mini or jumbo). You can make it in jumbo cups (should make about 1/2 the number of egg muffins) or mini cups (should make double the number) too, though. The baking time will be longer with jumbo cups, but I haven’t tested to confirm how much longer, so you’d have to check on them. Hope this helps!
Sandra
0This looks scrumptious! But I have a small problem….no fresh vegetables at the moment. Can frozen veggies (both broccoli & cauliflowers) be roasted in the oven at first? If so, how is this done? I realize that there will be a lot of moisture released if roasted. Or, should they be cooked in the microwave first, patted dry w/paper towels, and then be roasted until they are a bit browned? Going to try this, and even if they don’t “look pretty”, they still will be edible.
Wholesome Yum D
0Hi Sandra, You can use my roasted broccoli and cauliflower recipe, there is a section on roasting from frozen.
Dianne Lozier
0Too many pop up adds. Never saw list of ingredients. Tedious money maker ad loaded site.
Dianne Lozier
0Very interesting that you modify my comments or simply refuse to post. This certainly keeps your ratings up.
Wholesome Yum D
1Hi Dianne, I approve all comments on my website to keep out spam, so comments do not post right away. Ads keep the Wholesome Yum website running and allow me to develop recipes that readers like you can access absolutely free. However, you may be interested in Wholesome Yum Plus, which includes an ad-free version of the website, along with other perks. Also, for next time there is a jump to recipe button that takes you right to the recipe card.
Patricia A Hiles
0I absolutely love all your recipes. I have made many of them and my family enjoys the results also!
Sherry Stark
0Just wanted to wish you a (belated) Happy Birthday Maya!
Maya | Wholesome Yum
0Thank you so much, Sherry!
Sandra
0We love these veggie egg muffins! I will definitely make them again. Great job Maya for providing this recipe and for all your helpful hints and instructions.
Sally Tysinger
0How long can you keep these muffins if there are only 2 of you eating them…can they be frozen?
Wholesome Yum D
0Hi Sally, There is a whole section in the post on storage instructions.
Christie
0Delicious.
Bernice
0Such a great way to start the day. Thank you for the great breakfast recipe.
Jenni
0This was a great recipe! We have been using this as a meal prep breakfast and my kids and husband love it! Add some fruit and DONE!
Glenda
0They’re like delicious little on-the-go omelets! So satisfying! Thanks for sharing the recipe.
Toni
0These muffins are so fun to make and so delish! Everyone loved it!
Cathy
0Loved them. Made different variations for different tastes and will be making them regularly!
April
0These were delicious! Like little mini omelettes. My kids loved them!
Jess
0These egg muffins are a game changer for a quick morning breakfast! Thank you for sharing this recipe and making my morning routine so much easier.
Yessenia
0Oh my goddess delicious!!! Loved it.
Thomas Westheimer
0I partially cook bacon and line the sides of each cup. Sometimes I put 1 piece of pepperoni to “line” the bottom too
Tara
0What delicious egg muffins! I love the minimal prep and that they can be made ahead of time. Yum!
Anjali
0These egg muffins turned out so well!! They were super easy to make and were a great grab-and-go breakfast for us all week long!
Claudia Lamascolo
0I make these all the time its a great recipe and perfect to make ahead and freeze I pop on in the air fryer and they taste just like I just made them thanks for this recipe
Carol kingsolver
0Hi, I’m the only one in my household who is keto and will eat keto recipes. How do I make this recipe for just 4 egg cups? What are the ingredient measurements?
Wholesome Yum D
0Hi Carol, In the recipe card you can change the serving size to 4 and that will change the amounts of the ingredients for you.
rika
0I love these egg muffins. The perfect addition to my morning breakfast! Yum
Mike
0Easy peasy and delicious. I made mine with onion, cherry tomatoes, chopped sun dried tomatoes, apple wood bacon, cheddar cheese with a sliced breakfast sausage on top. Yum
Shanna
0These were so yummy! I added a little spinach to them.
Donae
0My husband and I love this recipe. I didn’t have any cauliflower so I used broccoli, frozen spinach squeezed dry, onion and sun dried tomato. It turned out great and was delicious! Next time I will spray my paper muffin liners. It did stick to the liners a bit.
Jill
0I love this recipe! It’s so simple & makes for such a great breakfast prep leaving you more time in the morning to do other things. I’m not paleo so I did add some shredded cheddar although Maya’s right it’s really not needed nor would it be too missed. I also added hemp seeds for a plant protein boost 🙂
Peggy
0can you add ground breakfast sausage to the recipe
Wholesome Yum M
0Hi Peggy, Yes, that sounds great! Enjoy!
Toni
0Love this recipe. I have to tweak a little bit because of my stomach issues. You gave some great tips about roasting the veggies first. And the coconut milk. Thanks!!
Kathy M
0Hi Maya!
Do you have any storing and reheating tips for these muffins? Can they be frozen?
Maya | Wholesome Yum
0Hi Kathy, You can keep them in the fridge for about week. You could also freeze them, but the texture is not great. You can reheat them in the microwave or in the oven.
Eman
0I am so happy to see this kind recipes✨
But is this recpes sut for kids ?
I mean age 1year ?
Maya | Wholesome Yum
0Hi Eman, I can’t give advice on what to feed your kids, but mine ate these at 1 year!
Sarah
0Hi Maya, thanks for a simple and tasty looking recipe. Have you tried making these with coconut milk instead of coconut cream? I’m currently out of coconut cream (it goes fast in my household!) and wondering if coconut milk will do the trick? Thanks so much! 🙂
Maya | Wholesome Yum
0Hi Sarah, Coconut milk should be fine – use the thick kind in a can.
Mimi
0Started eating “Keto” 7 weeks ago. Have tried other from-scratch muffin recipes and prepared mixes too and this recipe is hands down the best tasting and the easiest! So happy to have found you! Looking forward to trying many more of your recipes Maya!
Maya | Wholesome Yum
0I am so happy you liked the egg muffins, Mimi! Have a great day!
Lisa
0What a tasty recipeee!! Thank you for sharing!
Maya | Wholesome Yum
0I am so happy you liked the muffins, Lisa! Thanks for stopping by!
Kimberly Baxter
0Made this for dinner last week. So good! Thanks for the recipe.
Maya | Wholesome Yum
0I love to hear that, Kimberly! Thanks for stopping by!
Wholesome Yum A
0How long will these last in the refrigerator?
Maya | Wholesome Yum
0Hi Amanda! These will last 4-5 days in a sealed container in the refrigerator. I hope you like them!
Liz
0Hi! Can these be frozen and microwaved?
Maya | Wholesome Yum
0Definitely! I do that all the time. 🙂
Heather | Made In A Pinch
0These are great! I always need something to make and grab in a pinch, and these do the job! Thank you for the recipe!
Maya | Wholesome Yum
0Thank you, Heather! I’m glad you like them.
Lexie
0Yum. I love that these are full of veggies! I tried something similar with lunchmeat used as the muffin pan liners once and they were pretty great.
Thanks for sharing!
Maya | Wholesome Yum
0Thank you, Lexie!
Frees Lois
0Can these be frozen and reheated?
Maya | Wholesome Yum
0Yes!