Healthy Breakfast Egg Muffins

You are going to high five and hug yourself every rushed morning and mid-afternoon hanger-time for filling your freezer with these Healthy Breakfast Egg Muffins! You can pop these wholesome, filling muffins into the microwave and reheat them whenever you need a fast, filling breakfast or snack.

Healthy Breakfast Egg Muffins. Easy, low carb, and freezer friendly, these healthy egg muffin cups are the perfect make ahead breakfast. Like mini quiches without the crusts! Add spinach, ham, or any favorite veggie. Delicious with or without cheese, so these can be Paleo, Whole 30, and dairy free too!

Breakfast Egg Muffins are baked egg cups (or mini frittatas, if you prefer a slightly fancier name) that are loaded with any variety of fresh vegetable, meat, and/or cheesy additions you please.

I’ve made few versions of these freezer-friendly egg muffins over time, and while each of them has a tasty place in my heart, today’s suggested combo of Egg Muffins with spinach, feta, and a colorful array of veggies is my long-standing favorite.

Healthy Breakfast Egg Muffins. The perfect make-ahead, high protein breakfast! These egg muffin cups are packed with veggies, which means they're great for clean eating breakfasts and snacks.

How to Make the Best Breakfast Egg Muffins

A great egg muffin is all about finding the right ratios.

  • Egg-to-Veg Ratio: The goal here is to ensure that each of the breakfast egg muffin cups packs a feel-good serving of vegetables without a) falling apart or b) resembling a mini salad.

I consider myself a vegetable enthusiast, but even I have my limitations before 10 a.m.

  • Whole Egg to Egg White Ratio: After a few attempts—all of which were eaten right away or frozen for later in the name of “research,” but some of which were more delicious than others—I’ve determined the ideal whole egg to egg white ratio is 6 whole eggs + 4 egg whites.

Adding a few additional egg whites makes the muffins high in protein and low carb, without losing their filling, creamy texture. I would not recommend all egg whites, as this will cause the egg muffins to fall apart.

If you are looking for an egg muffin zero carb recipe, consider changing up the mix-ins you add to get the carbs down even more, or check out these Zero Carb Egg Muffins, which are higher in fat—it depends upon what exact ratio meets your needs, so feel free to play around.

Spicing It Up

Because egg-white-heavy recipes can be—there really is no polite way to say this—SO BORING, we need to jazz these egg muffins up with plenty of herbs and spices.

  • Dried Spices. My pantry staple go-tos are dried basil and dried oregano. The combo gives the breakfast egg muffins an Italian-inspired flair and complements the vegetables and feta.

If you are looking to cook more healthfully and share my sentiment towards bland food (no thank you!), dried herbs and spices are some of the most excellent tools you can use. They infuse recipes such as these healthy egg muffins with excellent flavor, without excess fat or calories.

  • If you like your egg muffins on the spicy side, you can also add a few dashes of hot sauce or pinch of cayenne.
  • For a zippy punch, try adding a few teaspoons of Dijon mustard.

Healthy Breakfast Egg Muffins. Spinach, veggies, and cheese make these egg muffins tasty. Easy to adapt for Paleo, Whole30, and dairy free!

Egg Muffin Filling—A Choose-Your-Own-Egg-Cup Adventure

Once you have your egg base, you can add any number of mix-ins.

  • Vegetables. The non-negotiable. Because I want the egg muffins to be filling and healthy, I always include a good amount of fresh vegetables like spinach and tomatoes.

You’ll feel great starting your day with a serving of veggies, and if you want to bring the egg muffins to the office for lunch, it makes them a more complete meal.

  • Meat. Tasty but optional.

I found the breakfast egg muffins plenty satisfying with veggies alone, but if you’d like to add meat, feel free to make these breakfast egg muffins with bacon (I highly recommend this method of baked bacon for the best results and easiest cleanup) or fold in diced cooked ham.

  • Cheese. Also tasty. Also optional.

You can swap the feta in this egg muffin recipe for any other cheese you enjoy (a cheddar version I made in my experimental attempts was delightful).

For dairy-free, Whole 30, or Paleo egg muffins, simply omit the cheese.

Healthy Breakfast Egg Muffins with spinach, bell peppers, and cherry tomatoes. This delicious recipe is easy to adapt to add more protein, such as breakfast egg muffins with bacon, or swap different veggies!

How to Store, Freeze, and Reheat Breakfast Egg Muffins

These Healthy Breakfast Egg Muffins will last up to three days in the refrigerator and three months in the freezer.

  • To Store in the Refrigerator: Let the egg muffins cool completely, then place them in an airtight container. You can store all of the egg muffins together in a single larger container or portion them into individual containers to take with you on the go. Plastic wrap and even plastic baggies work well for portability too.
  • To Store in the Freezer: Let the egg muffins cool completely, then individually wrap them in plastic wrap. Place in a ziptop bag, then freeze.
  • To Reheat Egg Muffins from Refrigerated or Frozen: Unwrap the muffins if needed. Place on a microwave-safe plate. Reheat gently in the microwave until hot and warmed through to the center, about 30 seconds (from thawed) or 1 to 2 minutes (from frozen).

The exact cook time you need to reheat the breakfast egg muffins will vary based on your microwave’s power. Consider the first egg muffin a bit of an experiment. From there, you’ll forever know how long you need.

More Healthy Muffin Recipes to Stock in Your Freezer

Healthy Breakfast Egg Muffins. Easy, low carb, and freezer friendly. Make ahead for quick, nutritious breakfasts that the whole family will love!

Recommended Tools to Make Healthy Breakfast Egg Muffins

Healthy Breakfast Egg Muffins. Easy, low carb, and freezer friendly, these healthy egg muffin cups are the perfect makeahead breakfast. Like mini quiches without the crusts! Add spinach, ham, or any favorite veggie. Delicious with or without cheese, so these can be Paleo, Whole 30, and dairy free too!
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Healthy Breakfast Egg Muffins

Yield: 12 muffins
Prep Time:
15 mins
Cook Time:
25 mins
Total Time:
40 mins
Healthy Breakfast Egg Muffins. Easy, low carb, and freezer friendly, these healthy egg muffin cups are the perfect make ahead breakfast. Add spinach, ham, hashbrowns, or any favorite veggie. Delicious with or without cheese, so these can be Paleo, Whole 30, and dairy free too!


  • 1 cup lightly packed baby spinach — chopped
  • 3/4 cup finely diced red bell pepper — about 1 small pepper
  • 3/4 cup finely diced green bell pepper — about 1 small pepper
  • 3/4 cup quartered cherry tomatoes — or grape tomatoes, about 1 cup whole tomatoes
  • 6 large eggs
  • 4 large egg whites
  • 1/4 teaspoon kosher salt
  • 1/4 teaspoon dried basil
  • 1/4 teaspoon dried oregano
  • Pinch ground black pepper — or cayenne pepper if you like a little kick!
  • 1/4 cup crumbled feta cheese — plus additional to sprinkle on top
  • Optional toppings: avocado — salsa, hot sauce, freshly chopped parsley


  1. Place a rack in the center of your oven and preheat to 350 degrees F. Lightly coat a standard 12-cup muffin tin with nonstick spray. Divide the spinach, red bell pepper, green bell pepper, and tomatoes among the cups (they will be about two-thirds of the way full).
  2. In a large bowl or large measuring cup with a spout (my favorite because it makes the mixture easy to pour), briskly whisk together the eggs, egg whites, salt, basil, oregano, and pepper until well combined. Carefully fill each muffin cup three-quarters of the way to the top with the egg mixture. Sprinkle the feta evenly over the tops of the cups.
  3. Bake for 24 to 28 minutes, until the egg muffins are set. Let cool for a few minutes, and then run a butter knife around the edges of each muffin to loosen it. Remove them from the pan and enjoy immediately, or let cool on a wire rack and refrigerate or freeze for later (see notes for more details).

Recipe Notes

  • Store leftover egg muffins in an airtight container or ziptop bag in the refrigerator for up to 3 days or individually wrap and freeze for up to 3 months. Reheat gently in the microwave (once thawed or directly from frozen) until hot and warmed through to the center, about 30 seconds (from thawed) or 1 or so minutes (from frozen), depending upon your microwave.
  • This recipe is incredibly flexible. Feel free to swap the listed veggies for the same amount of any other diced vegetable or cooked, diced meat. If the vegetables are very firm, such as carrots or sweet potatoes, I recommend cooking and cooling them first before adding them to the cups.
Course: Breakfast
Cuisine: American
Keyword: Easy Breakfast Recipe, Healthy Breakfast Egg Muffins

Nutrition Information

Amount per serving (1 muffin) — Calories: 70, Fat: 3g, Saturated Fat: 1g, Cholesterol: 96mg, Sodium: 148mg, Carbohydrates: 3g, Fiber: 1g, Sugar: 2g, Protein: 8g

Did you try this recipe? I want to see! Follow Well Plated on Instagram, snap a photo, and tag it #wellplated. I love to know what you are making!

This post was originally shared in February 2018 in partnership with McCormick Spices. It was republished with additional helpful content and a step-by-step recipe video.

This post contains some affiliate links, which means that I make a small commission off items you purchase at no additional cost to you.

About Erin Clarke

I’m fearlessly dedicated to making healthy food taste incredible. Wearer of plaid, travel enthusiast, and firmly convinced that sweets and veggies both deserve a place at the table. MORE ABOUT ERIN…


  1. Dear Erin, I love your blog and have been reading it for quite some time now. I enjoy cooking and also reading about cooking so I deeply appreciate that you post so regularly (and with no adds in between the recipes – thank you again!). I am big fan of your rosted carrot soup, so simple and it is one of the vegetables I always have at home (it resolves the thursday dinner crises). I will defenitely make these muffins since we have recently started to host and get invited to brunchs and I am always looking for healthy and tasty ideas. Greetings from another country and continent and keep up with your excelent work!

    • Thank you so much, Caroline! I so appreciate your taking the time to leave this thoughtful comment. I hope you enjoy the muffins too!

  2. Hi Erin. Please share why the egg whites are needed? I’m guessing as a “binding agent”? Can I make these without the egg whites? I’m learning. I can’t wait to make these! Happy Friday!!! 

    • Hi Andrea, I use egg whites to up the protein content in this recipe (they are the most protein-rich part of the egg), but you can use 2 additional whole eggs in place of the 4 egg whites if you prefer not to have extra egg yolks left over. I hope you enjoy!

  3. thank you for this, have been eating essentially most of these ingredients every morning as part of a routine, but would like a break every once in a while, love the idea of making ahead and freezing these

  4. Nicely done Erin! Most people don’t have the time to mess about in the kitchen in the morning so making a tone of these would be perfect! (:

  5. Had these for breakfast today. Kept me full, and I felt like a superstar eating veggies in the morning.

    • YAY!! So happy to hear this Elizabeth. Thank you so much for taking time to let me know <3

    • Jennifer Vaillancourt Reply

      Im about to food prep these now for the weekend, next week. I see you already answered my first question about using 6 whole eggs! Thanks for that! My other question is if I should use those little muffin tin liners or olive oil as a substitute as I am out of cooking spray. My instinct says use a light coat of olive oil. Lastly, many recipes ive read say to not salt eggs while cooking as it breaks down the proteins….but with the added veggies I think it really does need to be included prior to cooking. Do you think it matters? Should I just salt the veggies and not salt the egg mixture? Thanks for your advice!

      • Hi Jennifer! I’d brush the pans with olive oil. That should work fine. And I haven’t heard that about salt to be honest. I love it for flavor here, though you can sprinkle salt on afterwards if you prefer. I hope you enjoy them!

  6. These are SO CUTE! We’re always looking for something different for breakfast instead of same old, same old. This is clearly a way to use some leftover veggies (if they make sense, of course) but the recipe as it stands will be good for us! And to be able to make ahead is a huge selling point. Have a great weekend.

  7. Delicious! Now I know what I am going to bake for breakfast next week. Thank you!

  8. These would be perfect to bring to work for breakfast! Great recipe. I like feta, but I LOVE cheddar, so I’ll probably try that version.

  9. Made these for a brunch this morning and they were a hit! I did sauté the veggies a little bit to make sure they’d be soft and they were excellent. Thank you for yet another perfect recipe! 

    • Allison, I am SO excited to hear this, thank you!!! I’m so happy you all loved them. Thanks for taking time to leave this wonderful comment too!

  10. This is the perfect meal prep for this week’s breakfast!

  11. I love these SO much!!!! Perfect for on-the-go!

  12. So I made these little guys this morning for breakfast – SO GOOD! I did add a small amount of finely chopped onions and also some bacon that I’d fried and crumbled ahead of time. I made 6 of them with feta and 6 with sharp cheddar; both equally as tasty. This made a very adequate breakfast with a piece of oat nut toast. Thanks for a handy make-ahead recipe.

    • Your additions sound delicious, Chris! I’m so glad the recipe is a winner—thanks for taking the time to try it and report back!

  13. Would these be diabetic friendly? Newly diagnosed and searching for breakfast ideas, when these beauties popped up on my search! 

    • Hi Michelle, the recipe does seem to fit in with many of the guidelines, but since I don’t have a medical background, I’d check with your doctor or nutritionist if you have specific questions or concerns about the recipe. I’d hate to give you advice that isn’t correct and want to be safe!

  14. Can you freeze these

    • Hi Leslie, yes, you can! Check out the directions in the notes section, just below the recipe. I hope you enjoy!

  15. I’d like to serve these at a baby shower brunch, but would like to make them the evening before. Do you think they would reheat well in the oven without drying out?

    • Yes Jo, I think that would be fine! You could even make a test batch just to make sure you’re happy with the final texture. A little extra cheese would help keep them from drying out too. Otherwise, you could prep all the filling ingredients the day before, then just stir everything together and bake the morning of.

  16. Patricia Steixner Reply

    Love these! I’m always in a hurry and sometimes forget to eat breakfast. I used queso fresco instead of feta, it’s a little too strong for me and yum! Thank you

  17. Very tasty and satisfying.  My teenage daughter loves these.  I also made using kale instead of spinach.  Thanks for sharing recipe.

  18. Hi Erin. These look great! I was just wondering (since I can’t have lactose) what can I use instead of the feta cheese, or can I skip this ingredient all together? Thanks! Love your blog!

  19. very tasty satisfying to all. I love it.

  20. I sprayed my muffin tins of really well and these all stuck really badly. Destroyed. So frustrating because I was making them for a group event where I had signed up to bring food and now I’ve got nothing to bring.

    • Hi Shauna, I’m sorry to hear the muffins stuck to your tin—it can really depend on the type of tin and quality of the coating sometimes. I know it’s disappointing to try a new recipe and not have it come out, so I truly wish it would have worked better for you!

  21. Just wondering what you used to wrap the muffins before freezing. Thanks so much, can’t wait to try!

  22. Erin, have you made these in an instant pot? If so, would you please walk me through that? I’m an Instant pot newbie. Just made hard boiled eggs under my egg setting. So quick! And peeled amazingly!  Thank you!

    • Hi Jody, I have not made these in the Instant Pot, so I’m afraid I don’t have any specific advice to give on that front. I hope you love these if you give them a try!

  23. The veggie egg cups are an additional treat by adding a tablespoon of cooked quinoa in the bottom of the muffin cups with the veggies prior to baking. Ummmmmmn  LOVE UR SITE!!

  24.  I made these and they looked  fluffy and great coming out of the oven, but shortly after they deflated. Any idea why? Thank you. 

    • Hi Theresa! The muffins are by nature fairly flat. They are more like mini omelette cups versus a tall, domed bakery type of muffin. I hope you enjoy them!

  25. These are incredible! Thank you for the recipe! I made these egg cups yesterday for the first time after hearing about your website in my Weight Watcher’s community. Your egg cups are all the rage! I used low fat feta and they taste delish. Today, I “splurged” and added, as you suggested, salsa and avocado. I found that I could skip my mid-morning snack, because I was so full from breakfast! I love the fact that I could sneak an extra portion of veggies into my diet. These cups reheated really well for me. I can’t wait to explore the rest of your site to see what other yummy, healthy goodies I can round up! Thank you, Erin!

    • Sarah, I’m so happy to hear these were a hit! I’m so glad to have you as a reader, and I hope you find many more new favorite recipes to try!

  26. Can I use the 100 % egg whites in the carton? I had bought those for a similar recipe but this one sounds way better.

    • Linda, yes! You can swap the egg whites called for in the recipe for the egg whites in the carton. The carton should suggest an amount per white. I would use the whole eggs called for in the recipe though to make sure your muffins have enough structure. I hope you enjoy!

    • I’ve made a version of these egg muffins and all the comments are spot on, they are wonderful! I have added a layer of cooked red quinoa and this ups the fiber, protein and crunch factor. YUMMY!!

  27. Hello Erin and thank you for your beautiful recipe!
    Is there a way to prevent the egg muffins from deflating when I get them out of the oven?
    The are so big and puffed while in the oven,and in minutes after they are out,they lose most of their volume.
    What is the problem?
    Thank you again

  28. Hi Erin! These look delicious & I can’t wait to make. Could I sub frozen veggies for the fresh ones? If so, should they be cooked first? Thank you!

    • Hi Jen, you could precook them or let them thaw and pat them thoroughly dry with a paper towel. (Frozen veggies tend to give off a lot of moisture.) I haven’t tried using frozen veggies myself, but if you decide to experiment, I’d love to hear how it goes!

  29. Looking forward to trying this! Just want to let you know though that the Cabot’s cheese pop up ad is so obstructive that it is deterring me from looking at anything else on the blog :/

    • Liz, I am sorry for the hassle! It should have a clear way to close it (a video pop up might take a few seconds to display it, but there will be a clear “close” button). Let me know it doesn’t!

  30. Hi Erin, I have a pretty old muffin tin so i’m not sure how much they will still stick even if i use alot of nonstick spray. Can I put the paper muffin cups in the tin instead and bake the mixtures in there to be safe?

    • Hi Claire! I haven’t tried paper liners, but it could possibly stick to those too. You are welcome to experiment, but I still recommend being generous with nonstick spray. I hope it works!

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