Breakfast Egg Muffins (Easy Keto Recipe!)

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This Breakfast Egg Muffins recipe is keto, low carb, and perfect for busy weekday mornings. It is a healthy, high-protein recipe that is so easy to make! Made with eggs, almond milk, fresh spinach, tomatoes, green onions, cheddar cheese, and a bit of avocado (if you want!). Learn how to make homemade egg cups with this simple make-ahead recipe.

Overhead view of six Breakfast Egg Muffins cooling a on wire rack set above a dark background.

These nutritious, portable egg muffins are like mini frittatas or handheld omelettes. They are high in protein and low in carbs, making them the perfect healthy breakfast-on-the-go.

How to Make Breakfast Egg Muffins

This simple keto recipe is made with eggs, almond milk, fresh spinach, tomatoes, green onions and cheddar cheese. The best part of all is that the recipe is so effortless!

All you do is mix together all of your ingredients, pour them in a muffin pan and then bake until the egg muffins are set. I also like to top them with some sliced avocado (to add more healthy fats and also for presentation) when I am ready to serve or eat them, but that is completely optional.

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How to Store, Freeze, and Reheat Breakfast Egg Muffins

These Breakfast Egg Muffins are great for meal prepping on Sundays because you can make a batch, store it in the fridge and enjoy it for the next few days. They are also ideal for a brunch buffet, as you can make them ahead of time and reheat when you are ready to serve. They can be stored for up to three days in the refrigerator and three months in the freezer (just remember not to add the avocado, if using, until you are ready to eat them!)

  • To Store in the Refrigerator: Allow the egg muffins cool off completely, then place them in a sealed, airtight container. You can store all of the egg muffins together in one large container or portion each one into individual containers. Alternatively, you can wrap the egg muffins in plastic wrap or store them in zipped-top plastic bags.
  • To Store in the Freezer: Allow the egg muffins cool off completely, then wrap each one individually in plastic wrap. Place them in a freezer-safe zipped-top bag and place in freezer.
  • To Reheat from Refrigerated or Frozen: Unwrap the muffins, if needed, and place on a microwave-safe plate. Reheat in the microwave until warmed through to the center, for 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 the power of your microwave.

Close-up overhead view of Breakfast Egg Muffins cooling a on wire rack set above a dark background.

More Healthy Breakfast Recipes to Try

Here are some more nutritious morning meals to try out:

For this Breakfast Egg Muffins recipe, I recommend:

Here are a couple of tools I suggest using when making this recipe:

  • Box grater – You can save a ton of money by grating a brick of cheese yourself, rather than buying pre-shredded cheese. Pre-shredded cheese also contains additives that prevent the cheese from sticking together in the bag. So if you grate the cheese yourself, it will melt better too!
  • 6-cup muffin pan – This pan is the perfect size for this recipe. I love using it because its small enough to fit inside of my toaster oven, which heats up so much faster than my actual oven!

If you make this Breakfast Egg Muffins recipe, let me know! Leave a comment with a star rating ★ below, because I love hearing from you! ♡

Breakfast Egg Muffins (Easy Keto Recipe!)

Overhead view of Breakfast Egg Muffins cooling a on wire rack set above a dark background.
These Breakfast Egg Muffins are keto, low carb, and perfect for busy weekday mornings. A healthy, high-protein recipe that is so simple to make!
Alia Kay
5 from 5 votes
Prep Time 10 minutes
Cook Time 20 minutes
Total Time 30 minutes
Course Breakfast
Cuisine American
Servings 6 egg muffins
Calories 93 calories


  • 6 large eggs
  • 1/4 cup almond milk
  • 1/2 cup chopped fresh spinach
  • 1/3 cup chopped fresh tomatoes
  • 1/3 cup shredded cheddar cheese
  • 2 green onions, sliced
  • Optional topping: Sliced avocado


  • Preheat the oven to 350°F. Grease a muffin pan with cooking spray.
  • In a large bowl, whisk together the eggs, milk and a pinch each of salt and pepper.
  • Stir in the spinach, tomatoes, cheese and green onions.
  • Divide the mixture evenly between 6 muffin pan cups. Bake for 20-25 minutes, or until the muffins are set and firm in the center.
  • Remove the muffins from the oven and allow them to cool for 5 minutes in the pan, then use a butter knife to loosen the muffins from the cups. Serve warm, topped with avocado if using.


Nutrition Facts
Breakfast Egg Muffins (Easy Keto Recipe!)
Amount per Serving
% Daily Value*
Saturated Fat
Vitamin A
Vitamin C
* Percent Daily Values are based on a 2000 calorie diet.


  1. If you can, I highly recommend using organic, pasture-raised eggs in this recipe for maximum health benefits.
  2. Leftovers can be stored in an airtight container in the refrigerator for up to five days.
Keyword Breakfast Egg Muffins, Keto Egg Muffins

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Rate This Recipe:

5 from 5 votes (2 ratings without comment)


  1. 5 stars
    I made these on Sunday and they were absolutely delicious. I added avocado as well as some hot sauce. The whole family loved them. Thank you!

        1. Hi Linda! Yes, these egg muffins will last for up to three months in the freezer. To reheat them from frozen, you can heat them up in the microwave for 1 to 2 minutes. 🙂

    1. Hi Marianne! I don’t recommend cooking these egg muffins in the microwave. But if you have a toaster oven, you can definitely cook them in there. Just follow the recipe exactly how it is written. 🙂

    1. Hi Sara! To reheat the egg muffins, you can just place them in a baking dish and then heat them in a preheated 350°F oven or toaster oven for about 10 minutes. 🙂