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Breakfast Egg Muffin Recipe (Mini Frittatas)

This Healthy Egg Muffin Recipe is the perfect make-ahead grab-and-go breakfast! Think of it like a handheld version of your favorite frittata. Mix and match the ingredients to make the breakfast egg muffins your own, and enjoy a protein-packed, low-carb, gluten-free, nutrient-rich breakfast. 

An egg muffin with a bite taken out of it stacked on another muffin.

What Are Egg Muffins? 

Egg muffins, or mini frittatas, are like mini omelets. They feature a base of whisked eggs and various fillings. However, instead of cooking in a skillet, egg muffins cook in a muffin pan. 

As a result, they’re bite-sized, quick to prepare, and easy to clean up. Plus, unlike most omelet or frittata recipes, they’re great to make in bulk and store well, meaning they’re great for meal prep! 

Basic Ingredients 

Below is an overview of the ingredients and instructions for this recipe. Please be sure to scroll down to the recipe card below for the complete details! 

Ingredients for a breakfast egg muffin recipe on a white marble countertop.
  • Veggies – Use any veggies you like best and have on hand. Onion, zucchini, carrots, and spinach are some of our favorites! 
  • Large Eggs – These form the base of the egg muffins. 
  • Melted Butter – Substitute light olive oil if preferred. 
  • Coconut Flour – This adds a little structure, helping to create fluffy egg muffin cups that hold their shape. Do not substitute a different type of flour! 
  • Baking Powder – This helps the ingredients rise so your mini frittatas don’t fall flat. 
  • Seasonings – Garlic powder, salt, and pepper add a slightly savory taste. 
  • Cheddar Cheese – For the best taste and texture, buy a block of cheese and grate it yourself. 
Up close photo of an egg muffin with a bite taken out of it.

Flavor Options 

Feel free to mix and match all your favorite omelet ingredients! Some great mix-ins and variations include: 

  • Veggies – Mushrooms, tomatoes, red peppers, broccoli, or even boiled potatoes. 
  • Protein – Cooked ham, shredded chicken, breakfast sausage, ground turkey, or ground beef. 
  • Cheese – Monterrey, pepper jack, feta. 

How to Make This Egg Muffin Cups Recipe 

  1. Prepare. Before you begin, preheat your oven to 400 degrees Fahrenheit. Grease a silicone muffin pan with cooking spray, and set it aside. 
  2. Blend. Add the veggies and water to a blender or food processor, and pulse until smooth. 
  3. Whisk. Add the eggs to a large bowl, and whisk until smooth. Add the melted butter, coconut flour, baking powder, seasonings, and pureed veggies, and whisk to combine. 
  1. Bake. Pour the mixture into the greased muffin cups, and sprinkle the shredded cheese on top. Bake until the egg muffins are domed and slightly golden brown on top. 
  1. Cool. Let the mini frittatas cool slightly in the pan. Then, transfer them to a wire rack to cool completely, or enjoy them right away while they’re warm!  
Twelve baked egg muffins in a silicone pan on a metal sheet pan.

Storage Options 

  • Store leftover breakfast egg muffins in an airtight container in the fridge for up to 5 days. 
  • Freeze leftovers in a freezer-safe container or sealable bag for up to 3 months.
  • Reheat your egg muffins frozen or thawed in the microwave until warmed through. 

Common Questions About Egg Muffin Recipe

Why are my egg muffins rubbery? 

If your egg muffin cups recipe comes out rubbery, it’s typically because the eggs were overcooked. Keep a close eye on them, and remove them from the oven as soon as the eggs are set! 

How should I serve mini frittatas? 

These egg muffins are filling enough to enjoy on their own or with a side of fresh fruit. However, if you’re feeling extra hungry or want to serve them as part of a breakfast spread, try pairing them with options like fruit salad, easy banana muffins, sour cream rhubarb muffins, or protein donuts.  

Can I use all egg whites? 

We don’t recommend using all egg whites, because you lose quite a bit of flavor. However, if you want to give it a try, use 2 whole eggs and 6 egg whites. 

A breakfast egg muffin on a plate with two others topped with fresh parsley.

Breakfast Egg Muffin Recipe (Mini Frittatas) Recipe

This healthy breakfast egg muffins recipe is an easy, protein-packed, make-ahead breakfast that you can customize for all your needs!
Prep Time10 minutes
Cook Time30 minutes
Total Time40 minutes
Course: Breakfast
Cuisine: All American
Keyword: breakfast egg muffins, egg muffin cups recipe, egg muffin recipe, mini frittatas
Servings: 12 mini frittatas
Calories: 109kcal
Cost: $5.00

Equipment

Ingredients

  • 2 cups veggies, roughly chopped onion, zucchini, carrot, spinach, etc
  • 2 Tablespoons water
  • 8 eggs
  • 1/4 cup melted butter or light olive oil
  • 1/3 cup coconut flour
  • 1 teaspoon baking powder
  • 1 teaspoon garlic powder
  • 1 teaspoon salt
  • 1/4 teaspoon ground pepper
  • 1 cup shredded cheddar cheese

Instructions

  • Preheat the oven to 400F. Spray a silicone muffin pan with non-stick spray. Set the prepared muffin pan on a baking sheet.
  • In a blender or food processor add the 2 cups chopped veggies and 2 Tablespoons water. Blend until smooth.
    2 cups veggies, roughly chopped, 2 Tablespoons water
  • In a large bowl, add the eggs and whisk until smooth.
    8 eggs
  • Whisk in the melted butter, coconut flour, baking powder, garlic powder, salt, black pepper and pureed vegetables until combined.
    1/4 cup melted butter or light olive oil, 1/3 cup coconut flour, 1 teaspoon baking powder, 1 teaspoon garlic powder, 1 teaspoon salt, 1/4 teaspoon ground pepper
  • Pour the mixture into the 12 greased muffin cups and sprinkle the tops with shredded cheese. Bake for 30-35 minutes or until the egg muffins are domed and slightly golden brown on top.
    1 cup shredded cheddar cheese
  • Store leftovers in the refrigerator for up to 5 days or freezer for up to 3 months. Reheat in the microwave when ready to serve.

Video

Nutrition

Serving: 1muffin | Calories: 109kcal

Did you enjoy this Healthy Breakfast Egg Muffin recipe? We’d love it if you left a rating and review to let us know, and don’t forget to tag us in your recreations on Instagram!

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26 Comments

  1. I was looking for a filling food for a Candida cleansing diet, and these are just amazing! Thank you so much!!!

  2. These look so good! 2 quick questions for you:
    1. Can regular flour be used at all? Or does that really cause issues?
    2. Can these be frozen? Or just best stored in the frig?
    (OK, so that ended up being 4 questions….)
    Thanks for sharing this recipe. Love the fresh garden veggies – and love using the Magic Bullet too! 🙂

    1. Hi Amy! I would love to answer your questions!
      1. Coconut flour absorbs SO much liquid that regular flour is not a great option. Sorry! You can try and the muffins will still taste amazing, I just don’t think they will be as fluffy and light.
      2. Yes, these are great frozen! You can also store in the fridge for the week 🙂
      Let me know what you think after you make them. Thanks for stopping by and asking those great questions 🙂

  3. Love this, Sami! I do this for my daughter and I most mornings and she loves them. Great way to hide the veggies as well (I usually puree mine like you do as well!) Thanks so much for sharing 🙂

  4. These not only are perfect for a quick breakfast in the morning, they are adorable! That alone has to sell my tweens on eatting a healthy breakfast! Thanks so much for sharing with us at You Link it We Make It. We hope you’ll come back and link up with us again! – Kim @ knockitoffkim.com

  5. We eat so many eggs it became cost-effective to get our own chickens. 🙂 My kids love going out and getting the fresh eggs every day – and I love eating them! 🙂

    Your mini-frittatas look delish! I’m sure my family will love them! Thank you so much for sharing them with us at Allergy Free Thursdays!

  6. These look absolutely amazing! I’ve never specifically made mini frittatas before. However, I have made regular sized ones and omlettes in muffin tins. So, I’ve come close! I’m going to have to give these a try especially once the race is on to keep up with summer produce. Thanks for perfecting the recipe! I can’t wait to try it!

    1. Oh Gina, thank you so much for the kind words! You nailed it right on the head, when you are overrun with garden produce this is the recipe to make! I hope you enjoy them 🙂 It seems to me you are very familiar with egg muffins so this simple breakfast recipe will come be a cinch for you!

  7. Hi Sammi, These mini frittatas look so appetizing! I find it interesting also that you used coconut flour which soaks up liquid like a sponge! Well done! Blessings, Janet

  8. These look amazing and I love to have some simple healthy eggs on hand in the morning. I love to add kale to mind as well.
    Thanks for the recipe,
    Bev

  9. Frittatas are one of the most delicious breakfast ideas! Love the mini version – great for kids! Pinning and stumbling!

  10. VERY excited to try these, Miss Sammi. I love the concept of this but I don’t love the recipe I’ve used in the past. What type of muffin tin do you use? I’ve found that the one I have really cooks the outside too long so it’s kind of tough and burnt tasting.

    1. Johanna, thank you for asking this question as I completely forgot to add what muffin pan I use. I have updated the recipe so it is there now 🙂 I bought this silicone muffin pan along with a mini muffin pan from Amazon. http://amzn.to/29QulyR I still grease the pan even though it is supposed to be non-stick. I have had a mini frittata disaster when I didn’t. Ha! I sure hope you love this recipe! Let me know 🙂