Healthy Breakfast Egg Muffins (3 Ways)


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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 to 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 muffins in a muffin pan.

Healthy Breakfast Egg Muffins (3 Ways)

5 from 47 votes
Prep: 15 minutes
Cook: 25 minutes
Total: 40 minutes
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
Did you make this recipe?Mention @downshiftology or tag #downshiftology!

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Recipe Rating


  1. What should I do differently next time.. mine deflated while cooling and I ended up with thin dense muffins. 

    I lightly coated the inside cups of a nonstick muffin pan with avo oil. Then layered spinach, bacon, bell pepper, grated cheddar cheese, then whisked egg. Topped with ground black pepper and convection baked at 350 for 20 mins. They were puffy when I pulled them out then deflated.

    Note: after whisking the eggs I strained them before pouring into muffin cup. Any feedback would be great! Thank you.5 stars

  2. I’ve made this recipe in muffin tins, but I just got 1-cup Souper Cubes and I prefer the 1-cup, brick-shaped portions! Plus I can freeze them.

    Lisa, I’m recovering from surgery right now and over the last couple weeks, I used a lot of your recipes to do some make-ahead freezer meals to keep me nourished as I recover. I noticed when I was searching, there aren’t many good results for “recipes to eat while recovering from surgery.” Maybe you should make one! It could also appeal to people wanting to make food for a loved one after surgery.5 stars

    1. Thanks for the tip! I’ll consider that as a post, but hope you’re on your way to a speedy recovery Ali.

      1. I second this request. I will be having shoulder surgery in Nov. and could really use some good freezer recipes that my family can have in the freezer while I am out of commission. Thank you!

  3. I’m wondering how you avoid browning? I just have done something wrong as there was a brown film around the sides and bottom.5 stars

    1. Hi Sandra – a little browning is definitely normal. You could always reduce the temperature and cook them a bit longer. :)

  4. I made these egg muffins this morning. It was super easy to organise and do. I used all three of Lisa’s suggestions and made 18! They are great for freezing and having a quick meal to heat up when needed and also a great breakfast treat. What I love is the healthy ingredients that I can put in each muffin and know that my family is getting the goodness out of something that tastes delicious!

    Thank you Lisa!

  5. I went full meal prep with these babies! I made a full batch of 12 in each flavor combination so we could have them for breakfast a couple of days, and freeze the rest for later! Breakfast for busy working days sorted, thanks so much Lisa!5 stars

  6. I took these to a friend (the tomato, spinach and goat cheese variety) and her husband said they were the best egg muffins he had ever had.  And they were just gorgeous too!!  Thanks Lisa!
    5 stars

  7. First off, these are excellent. They’re simple, endlessly customizable, low-carb, freezable, and fantastic to make in bulk. The first few times I made them, they came out perfect, but then they started sticking like crazy, even though I was dutifully greasing the cups each time with olive oil spray and rubbing them down by hand to ensure they were properly coated.

    I was about to give up on these with batch after batch coming apart around the fillings, and then I found a tip that saved the day- grease the cups with an oil that’s solid at room temperature. Think butter, bacon grease, coconut oil, even shortening or lard. My problem was that the olive oil kept rolling down the walls of the cups and not staying put. I made a batch just now with the cups greased with butter, and they look perfect. And failing that, Trudeau makes an excellent silicone muffin pan.5 stars

  8. I bought the ceramic muffin pan and made a batch of these.  
    Do you spray the pan?  These stuck to the pan and made a huge mess coming out.  
    I love these and they’re so easy and I love having breakfast ready…. 

      1. I made these muffins following this recipe and they are so convenient to grab and go for work. I really liked the ideas of mixing the different types of meats, veggies, and cheeses for a variety of egg muffins. I too used a metal baking pan for this recipe; however, now I am inspired to purchase a ceramic one. Thanks again for blessing us with this recipe!!

        I liked the recipe so much, I signed up to receive the emails and I look forward to making more recipes!5 stars

      2. This ceramic muffin pan is my favorite and so easy to clean! Also, glad you’re loving this recipe as well, Regina.

    1. I had the same problem until I bought some silicone muffin liners.  I purchased the OXO brand individual liners but I would probably buy the whole silicone muffin tin if I were to do it over since you have to wash these individually although they haven’t tipped over in the top rack of the DW so far 👍🏻 Definitely a game-changer though when making egg muffins.  I just sprayed the silicone muffin liner with a quick spritz of vegetable oil spray and they do great!!

  9. Doing the whole30 meal plan this month and made the Italian sausage and kale egg muffins (without the cheese). Super easy and so delicious! Leftovers in the freezer for future meals.  Thanks! 5 stars