Healthy Breakfast Egg Muffins (3 Ways)

Egg muffins are a healthy, easy, on-the-go breakfast. They’re filling, low-carb, and perfect for meal prepping. Just switch up a few simple veggie and protein ingredients to create delicious combos that will last you through the week!

Egg muffins in a muffin pan.

The new year is finally here, which means it’s time to get back into healthy lifestyle habits. But for many, balancing a busy work life and setting healthy goals can sometimes seem intimidating. So today, I’m bringing back a simple recipe that will make breakfast a breeze: egg muffins.

Egg muffins are basically mini frittatas that are easily customizable. You’ve seen me make them before, with my zucchini and prosciutto egg muffins. But the flavor combinations are endless.

I’m sharing three new flavors today, but you can mix and match your favorite vegetables, meats and herbs and get creative. The best part? These little egg muffins are a protein packed breakfast that can easily be stored away and reheated in an instant.

Breakfast Egg Muffin Ingredients

Similar to making a frittata or scramble, all you need for these muffins are an egg base and some fresh ingredients. Here’s the breakdown.

  • Egg base: Simply whisk up a bowl of eggs and season with salt and pepper.
  • Vegetables: Now’s the time to sneak in more greens for breakfast! You can add in just about any vegetable such as spinach, kale, broccoli, or tomatoes. Just give them a quick saute or boil, then dice into small pieces before combining with the egg base.
  • Meat (optional): Looking to add some extra protein? Bacon or sausage are delicious options that pair well with any vegetable. Just pre-cook it before adding to the eggs.
  • Cheese (optional): From grated parmesan cheese to cheddar and goat cheese crumbles, the choice is up to you! You can add the cheese into the veggie and meat mix or sprinkle it on top, it’s up to you. *Note: If you want to keep this recipe dairy-free and Whole30 compliant, exclude the cheese.

Adding eggs to a bowl to make egg muffins.

Are Egg Muffins Low-Carb and Keto?

Given the ingredients above, egg muffins are a keto-friendly recipe. So if you’re looking for a low carb breakfast, this is definitely something you’ll want to whip up. But here’s a few things to look out for to keep this recipe keto:

  • No starchy vegetables. These are ingredients such as sweet potatoes, potatoes, corn, or peas.
  • Avoid processed meats. While I recommended bacon and sausage above, the keto diet favors non processed meats.

How To Make The Best Egg Muffins

Now that you have a basic understanding of what goes into these muffins, let’s get cooking. I’m sharing the base recipe for any egg muffin. But, in the recipe card below you’ll find three delicious flavors, including 1) broccoli, bacon and cheddar, 2) sausage, kale and parmesan, and 3) spinach, tomato and goat cheese.

  1. Whisk 12 eggs. Each muffins requires 1 egg to make. So, depending on how many muffins you are making – follow this general rule.
  2. Create your add-ins. Here you’ll have the choice of throwing in veggies, meats, or cheeses. But, to keep the ratio even with the egg base, you will need about 3-4 cups of add-ins for 12 muffins.
  3. Fill the muffin tray with ingredients. First add in your veggies and meats, then pour the egg mixture into each muffin until it reaches about 90% full.
  4. Bake at 350 degrees Fahrenheit for 20-25 minutes.
  5. Let the muffins cool. Then run a knife along the outer edge and remove each muffin.

If you watched my favorite cookware video you know I’m trying to get away from non-stick cookware and bakeware. I recently found the ceramic muffin pan you see in the photos and I love it.

Add the egg muffin ingredients to a muffin tin.

How to Store and Reheat

The best part about these muffins is that they make for an easy breakfast meal prep. You can make a batch on Sunday and enjoy them all week long.

Store them in the fridge for up to three days, or in the freezer for up to three months. Just make sure to place them in sealed containers or freezer-safe bags to keep them fresh.

To reheat, simply pop them in the microwave for about 30 seconds (from the refrigerator) or 1-2 minutes (from the freezer).

A variety of egg muffins on a table.

More Healthy Breakfast Ideas

Here are a few more healthy breakfast ideas to keep in your morning rotation.

Egg Muffin Recipe Video

While this recipe is easy to make, it always helps to watch a quick video. Give it a watch below!

Egg muffins in a muffin pan.

Healthy Breakfast Egg Muffins (3 Ways)

5 from 36 votes
Prep Time: 15 mins
Cook Time: 25 mins
Total Time: 40 mins
Servings: 12 servings
Author: Lisa Bryan
Egg muffins are the perfect on-the-go breakfast that's healthy, low-carb, and great for meal prep. Just switch up a few simple veggie and protein ingredients to create delicious combos that will last you through the week!


Egg Base

  • 12 large eggs
  • salt and pepper, to taste

Broccoli, Bacon & Cheddar

  • 4 cups broccoli florets
  • 3 slices bacon
  • 1 cup grated cheddar cheese
  • 1/4 cup chives, finely sliced

Italian Sausage, Kale & Parmesan

  • 1/2 pound Italian sausage
  • 1 shallot, finely diced
  • 3 cup (packed) kale, roughly chopped
  • 1 cup grated parmesan

Spinach, Tomato & Goat Cheese

  • 24 grape tomatoes, halved
  • 1 cup (packed) baby spinach
  • 1 scallion, thinly sliced
  • 6 ounces goat cheese


Egg Base - Same For All Flavors

  • Add the 12 eggs to a large 4-cup measuring cup and season with salt and pepper. Whisk the eggs until fluffy.

Broccoli, Bacon & Cheddar

  • Slice the bacon into 1/2-inch thick pieces. Add to a saute pan over medium heat, stirring frequently and cook until crispy. Use a slotted spoon to remove the bacon to a paper towel.
  • Fill a pot with 1-inch of water and bring it to a boil. Insert a steamer basket, then add the broccoli florets. Cover with a lid and cook for 5-6 minutes. Remove the steamer basket and broccoli, and let cool for a couple of minutes. Then dice the broccoli into small pieces.
  • Fill the muffin tray about 1/2 full with pieces of broccoli, bacon, and cheddar cheese. Sprinkle with chives. Then fill with egg mixture about 90% full and bake at 350F for 20-25 minutes.
  • Let the muffins cool slightly, then run a knife along the outer edge and remove each egg muffin. Enjoy immediately or store in the fridge or freezer.

Sausage, Kale & Parmesan

  • Add the sausage to a saute pan on medium heat. Use a spatula to break up the sausage and cook it until it's just browned.
  • If there's enough fat in the pan from the sausage, you might not need to add oil. But if the pan looks dry, add 1 tablespoon of olive oil. Add the shallot and kale to the pan and saute for 2 minutes, or until the kale has wilted. Then remove from the heat.
  • Fill the muffin tray about 1/2 full with the sausage kale mixture. Sprinkle some parmesan cheese into each muffin cup. Then fill with egg mixture about 90% full and bake at 350F for 20-25 minutes.
  • Let the muffins cool slightly, then run a knife along the outer edge and remove each egg muffin. Enjoy immediately or store in the fridge or freezer.

Spinach, Tomato & Goat Cheese

  • Roughly chop the baby spinach. Then, add a small handful of spinach to each muffin cup.
  • Add 4 grape tomatoes halves and a sprinkle of scallions and goat cheese. Then fill with egg mixture about 90% full and bake at 350F for 20-25 minutes.
  • Let the muffins cool slightly, then run a knife along the outer edge and remove each egg muffin. Enjoy immediately or store in the fridge or freezer.

Lisa's Tips

  • Nutrition information is based on the broccoli, bacon, cheddar flavor.
  • Each flavor listed in the recipe card has enough ingredients to fill a complete 12-muffin pan. You can always use less of each flavor combination and mix and match as I've done.
  • For the spinach, tomato, and goat cheese muffin, you might need to cook it 1-2 minutes longer, as there is more juice from the tomato.
  • If you are using a regular muffin tin, you can use an oil spray or silicone cups to take the muffins out. Just make sure to not use the paper cups as it will stick.


Calories: 134kcal, Carbohydrates: 3g, Protein: 9g, Fat: 10g, Saturated Fat: 4g, Cholesterol: 177mg, Sodium: 167mg, Potassium: 177mg, Fiber: 1g, Sugar: 1g, Vitamin A: 557IU, Vitamin C: 28mg, Calcium: 107mg, Iron: 1mg
Course: Breakfast
Cuisine: American
Keyword: breakfast egg muffins, egg muffin cups, egg muffin recipe, egg muffins
©Downshiftology. Content and photographs are copyright protected. Sharing of this recipe is both encouraged and appreciated. Copying and/or pasting full recipes to any social media is strictly prohibited.
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92 comments on “Healthy Breakfast Egg Muffins (3 Ways)”

  1. These are awesome! Sounds like a lot of people are having a hard time with the eggs sticking… parchment cups are the answer! They do not stick at all and are a game-changer for egg muffins.5 stars

  2. Love all theses flavor combos but my egg muffins had TONS of little tiny air pockets in them after they were baked. Any advice?5 stars

    • Hi Jennifer! Happy you loved the egg muffins! It sounds like you may have whisked a bit to much air into the egg mixture before cooking. That usually causes the air bubbles. Hope your next batch turns out even better!

  3. would this work with just egg whites

  4. These were delicious. Cooked them tonight. Only change I made to the recipe was to make them into mini quiches by cutting a pie shell into muffin size shells and putting the ingredients into the shells. So, so good. 5 stars

  5. This was so easy to make and perfect for my needs on the go. I like food I can grab literally in my home and not at the fast food joints. It bridges the gap between the electronic age and good nutrition. Thanks for the recipe. I do make mine with paper muffin cups as they have no clean up and fast set up. I must say i could spray light coconut oil for the egg recipe, but when I make my mini meatloaf muffins, there is enough oil that doesn’t really stick badly. No fear, eat well. Thanks for the great menu recipes.5 stars

  6. Just reviewing this recipe and see that you just put spinach in raw? You don’t recommend sautéing it before you put it in the cups? Thanks!

  7. Super easy to make and delicious. However, even though I greased the muffin tin, they stuck so badly to it that I think the tin is garbage because I can’t get the egg off.5 stars

    • Hi Blaine – I’m glad you enjoyed the egg muffins! It sounds like you may need a new tin, things usually stick once the non-stick surface is scratched or worn off.

  8. So glad I have found your website and Facebook page. You have a lot of great recipes! Just made your egg muffins and can not wait to try them. I have made some of your smoothies and anti inflammatory drinks, love them. Thank you for all the great recipes and ideas. 5 stars

  9. best recipe I have found for these!5 stars

  10. These recipes look really apatizising!!!!
    Thanks so much as I was looking everywhere for these recipes.

  11. This is my first time on Downshiftology. I really loved it. So many great recipe ideas. Thanks so much.5 stars

  12. My daughter loves these! We’ve made them numerous times and have changed up the ingredients. So easy. And my husband just made a variation of them for lunch today with our leftover turkey from Thanksgiving. :) Thank you, Lisa!5 stars

  13. Thanks for the recipe. They are wonderful. Even the kids love them. Greetings from Germany.5 stars

  14. I love this recipe and want to try it for a fall brunch. Please share the ceramic muffin pan brand. I tried the link and Amazon states the product is not available.

    • Hi Robin – Unfortunately I am not sure when they will re-stock the muffin pan! But I will be sure to find a similar one if I can.

  15. Loved this recipe. I bought a silicone muffin pan which made removal and cleanup a breeze. Currently doing whole30 so used compliant sausage and no cheese. Sautéed kale with onion and garlic and added as a base. Soooo good! Thank you! 5 stars

  16. Easy to make and tasty to eat. The best breakfast hack for a weekday.5 stars

  17. Dear Lisa,

    I was wondering about the nutrition guide, for me it is not obvious if it refers to the whole meal or just one serving.
    Thank you for your help! :)

  18. The perfect breakfast food!5 stars

  19. This recipe is so easy to make. If you have eggs to use this is the recipe you need. 
    I put what I had in my fridge : onions, bacon, finely minced Brussels sprouts, tomato, cheese and the batter I’ve added to the egg mix some cream and a pinch of nutmeg. You can put anything you have into it and make something so tasty and amazing. 
    You should give this recipe a try, you won’t be disappointed. 5 stars

    • Hi Audrey – Happy to hear you found this recipe easy to make! It’s such a great way to utilize any leftover ingredients you have in the fridge :)

  20. I made these last weekend and loved them, making another batch this week, thank you!5 stars

  21. Made ’em. Loved ’em. But cleaning my muffin tin is a NIGHTMARE! I don’t have a nonstick tin but coated it with avocado oil. Still, the egg is stuck on there, probably for life. Any hints on how to clean if off, and how to prevent this again? Thanks!

    • Hi Barbara – you could try soaking your pan in hot soapy water. But yes, many older or used non-sticks aren’t actually non-stick anymore. You could always line it with silicone muffin cups, or purchase the ceramic pan I mention in the video. It’s much healthier than non-stick as well. :)

      • Thank you! Apparently, you can even buy an entire muffin pan made of silicone. I finally cleaned my old metal pan by soaking it with water and vinegar, then adding baking soda, then using an SOS pad. Will never bake eggs in that pan again! Will try your ceramic pan.

        Love your recipes! You are my cooking guru!

      • Hi Barbara – Yes! Definitely try my ceramic pan and let me know how you like it :)

  22. I meal prepped the broccoli cheddar ones for breakfast this week and they turned out perfectly! Cooking time and temperature are perfect!5 stars

  23. THIS looks delicious!

  24. Hi Lisa! I have prepared the egg-muffins and they were perfect to take at work for lunch and they Tasten super 👍🏻 many thanks, Anne5 stars

  25. I’ve made these egg muffins twice: first with goat cheese, cherry tomatoes and mexican veggies, sprinkled with parmesan and second time with tuna, onion and green olives. Delicious !!!!
    It was super easy and fast, everyone loved it.5 stars

    • Hi Gabriela – I love your tuna version! That sounds amazing, I’ll definitely have to try that. But I’m happy you’ve been enjoying this recipe :)

  26. I have been meal prepping ever Sunday or so foe lunch. And i get breakfast at starbucks and I realized one day wow I spend a lot of money for a breakfast sandwich and coffee. Like almost $30 on breakfast. So i then started meal prepped breakfast. I was getting tired of hard boiled eggs 3 times a week and then oatmeal. I saw Lisa make these and I fell in love!! They are great, hardy and keep me full. I freeze them and take some out at night and microwave a few min and they are perfect. I had a ton on ingredients so they are very interchangeable. Perfect 5 stars

    • Hi Stacy – I’m thrilled to hear you’ve found a new recipe to throw into your breakfast rotation! These little muffins are such an easy and delicious way to get your protein and veggies in :)

  27. These muffins were so easy to make and totally Whole30 compliant without the cheese. Even my kids gobbled them up! Thanks!5 stars

    • Hi Michelle – It’s the best when you find recipes that are kid approved! Happy to hear you all enjoyed these muffins :)

  28. I made a bunch of these yesterday with the ingredients I had at home and now I have the perfect dinner for the week! So easy to reheat when I arrive late and tired from work.5 stars

  29. I loved these muffins. I made a spinach&tomato&goat cheese one on Sunday. So good. Thank you Lisa for always putting out the best for us! 🙂 p.s. i forgot to spray the muffin tin with oil, still they came out without problem. 5 stars

    • Hi Assem – Spinach, tomato, and goat cheese is my favorite combo :) But, I’m glad to hear your muffins still came out perfectly without adding oil!

  30. Loved these!! We did ours with carmelized onions, sautéed fresh spinach, and cut up Cajun chicken sausage (oh and some hot sauce to the eggs)—delish!! Love that this is low carb and that we can throw whatever we have into them! We are on our second batch this week!!5 stars

  31. Hey Lisa! I made the muffins! Love them! I actually made them for dinner with your bacin wrapped sweet potatoes fries. I will post a pic on your Instagram, you got to see them 😁 made them with special orders for family, everyone likes their own creation. Had to number the pan so each one would know who’s who….lol5 stars

  32. Our breakfast for this week and we are loving it ❤️. Thanks Lisa for another easy and healthy recipe. Hope you continue making for breakfast prep such as this one.5 stars

  33. What a fun, easy recipe! I tried this out with some family that came to visit for brunch last week and it went over great! Also, since I’m vegan and didn’t want to miss out, I tried making a variation with vegan cheese and vegan eggs – SO GOOD!
    Keep up the inspiration!5 stars

  34. I started looking at your vlog, then switched to Instagram for practicing healthy eating habits. I made those muffins during a long weekend from whatever I had in the fridge: smoked salmon, cherry tomatoes & spinach. I have been eating them two days. Delicious! And big thanks for what you do! :)5 stars

    • Hi Anna – I love your version of these egg muffins :) Can’t wait for you to start incorporating healthy habits for the new year!

  35. I made these with spinach, bacon and gouda cheese. They are amazing! I could barely wait for them to cool down before I started eating.
    They taste amazing and cook without making the egg “rubbery”. I’m not always the biggest fan of eggs but this is a game changer.
    New weekly staple here we go!5 stars

  36. I just made these today and will probably be making them every week to snack on them during the week. So easy, accessible ingredients, on budget meal! Love it!5 stars

  37. I made these egg muffins yesterday using onions, mushrooms, Canadian bacon, spinach, and cheese. They turned out delicious! Definitely easy to make and wonderful to have ready in the refrigerator to heat up and enjoy! 5 stars

  38. Hi, I love your site! I have made these before with all egg whites with no problem, however this round using whole eggs, my muffins had huge air pockets and felt like egg muffin tops not whole muffins that I could not slice through.

    Do you think the culprit is over beating the eggs?

    • Yes, over beating the eggs could certainly be the culprit. I’d give them another try! :)

      • I had the same problem and did not over beat the eggs. I tried again and made sure the middle was full enough in each one so they didn’t collapse in the center. The only thing is that I may have overfilled them a bit and couldn’t quite fit one egg per muffin, so I need to tweak it a bi next time to get it just right. They still taste great either way… I just wanted them to look pretty 😀5 stars

  39. I love these. Where did you find the muffin pans? Those are great because they look easy to clean.

    • Hi Paula – You can find the link to the ceramic pan under the section “How To Make The Best Egg Muffins”.

  40. Hi Lisa, I’m Victoria from Belfast Northern Ireland. I came across your youtube channel and im so excited to have a go at your ideas.. espesh the egg muffins! I struggle with coming up with nutritional dinner ideas and sussing out lunch ideas for my husband and I but having looked thru so many ‘meal prep’ videos, I am loving the look of yours. Thank you for sharing them. I was thinking I might use the egg muffin ones for lunch at work.. I work as a special needs classroom assistant and don’t get much time for lunch, so thought these will be handy to eat quick :) Will let you know how I go. Happy New Year.. Thanks again!!

    • Hi Victoria – I am so glad you discovered Downshiftology as well! Can’t wait for you to try my meal preps and new recipes coming your way this year :)

  41. These are so delicious! I love that I can customize each one to what my family likes. We usually add roasted red peppers to the veggie mix too. So much more budget friendly than stopping at Starbucks.5 stars

  42. I love Egg Muffins so much and your versions look delicious! Broccoli, Bacon & Cheddar for me please :)5 stars

  43. Mmm, I love the versatility of this recipe! I think I’ll go for the bacon version please!5 stars

  44. This is such a fun way to prepare breakfast. And with three different flavor options, everyone will get to choose their favorite. :)5 stars

  45. These were just delightful to create! I cleaned out my fridge and added all kinds of veggies, cheese, and meat. Thanks for this great low carb friendly recipe idea!5 stars