Easy Breakfast Egg Muffins With Cheese

Heather Dessinger

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Easy Breakfast Egg Muffins With Cheese

Do you have a kid that picks at scrambled eggs? Don’t tell our chickens, but my kids are completely over a light, fluffy plate of golden-yoked goodness. And omelettes. Annnnnd hard boiled eggs. It’s not that they’re picky eaters… it’s just that the hens have been overachieving all summer.

They will be laying fewer eggs soon as the weather cools, but for now I’m pulling out some old favorites to help us enjoy the rest of the season. Bacon egg cupsbacon tomato quiche, and these cheesy breakfast egg muffins are at the top of my list.

They only take about 10 minutes of hands-on time, are kid-friendly, and are a great way to make use of what I already have on hand.

I love serving them alongside gluten-free waffles for a lazy Saturday brunch, but they also make a super convenient grab-and-go breakfast option on busy mornings. 

Flavor Combination Ideas

Since they’re essentially just little omelettes baked in muffin cups, and you can use whatever veggies you like best. Some of our favorite flavor combinations are: 

  • Bell Pepper, Onion, Jalapeño & Zucchini
  • Baby Spinach, Tomato & Mozzarella 
  • Bacon & Cheese 
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4.10 from 10 votes

Breakfast Egg Muffins With Cheese

These healthy breakfast egg muffins only take 10 minutes of hands-on prep time, and they're perfect for a sit-down brunch or an on-the-go meal.
Course Breakfast
Cuisine American
Prep Time 10 minutes
15 minutes
Total Time 25 minutes
Servings 8 muffins
Calories 156kcal
Author Heather Dessinger


  • muffin pan


Base Recipe

  • 8 large eggs
  • cups cheddar cheese (or 3/4 cup cheddar and 1/2 cup parmesan cheese)
  • ¼ tsp sea salt

Flavoring Option 1: Bell pepper, Onion, Jalapeño and Zucchini

  • ¼ cup diced red bell pepper
  • ¼ cup diced red onion
  • ¼ cup shredded zucchini
  • 1 tbsp minced jalapeno (optional)

Flavoring Option 2: Baby spinach, Tomato & Mozzarella

  • ½ cup loosely packed spinach leaves
  • ¼ cup grape tomatoes (cut in half)
  • ¼ cup diced onion (red or yellow)

Bacon & Cheese


  • Preheat your oven to 400°F.
  • Place eight baking cups inside your muffin tin and set aside. 
  • In a large bowl, beat the eggs.
  • Mix in the cheese, salt, and chopped vegetables.
  • Divide the egg mixture evenly between the baking cups.
  • Bake in the preheated oven for 15-20 minutes, or until a toothpick comes out clean.
  • Serve warm and enjoy!


Nutrition values are estimated based on bell pepper, onion, jalapeno and zucchini, but you can use any combination of veggies you like. 
Although they’re best served fresh, leftovers can be stored in an airtight container in the fridge or freezer and then reheated. 


Serving: 1breakfast muffin | Calories: 156kcal | Carbohydrates: 1g | Protein: 11g | Fat: 11g | Saturated Fat: 5g | Cholesterol: 229mg | Sodium: 263mg | Potassium: 127mg | Fiber: 0g | Sugar: 0g | Vitamin A: 655IU | Vitamin C: 9.2mg | Calcium: 159mg | Iron: 1.1mg

More Healthy Breakfast Recipes To Try

Easy Breakfast Sausage – This sweet and savory maple breakfast sausage is super simple and mouthwateringly delicious.

Homemade Maple Granola – This grain-free granola is made with nuts and seeds and sweetened with maple syrup. It makes a yummy make-ahead breakfast for busy mornings. 

Coconut Yogurt – This creamy, thick dairy-free yogurt is an easy way to support immunity with probiotics, and you probably have everything you need to make it right now.

Do you ever make breakfast egg muffins? What is your favorite combination?

These healthy breakfast egg muffins only take 10 minutes of hands-on prep time, and they make a delicious grab-and-go breakfast.

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Heather is a holistic health educator, herbalist, DIYer, Lyme and mold warrior. Since founding Mommypotamus.com in 2009, Heather has been taking complicated health research and making it easy to understand. She shares tested natural recipes and herbal remedies with millions of naturally minded mamas around the world. 

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10 thoughts on “Easy Breakfast Egg Muffins With Cheese”

      • I wondered the same thing, so I froze some and warmed them up in the oven. They were okay, but they seemed a little soggy compared to when they’re fresh out of the oven. They would probably be fine if I’d left them in for a little longer to get rid of the excess moisture, but we had a schedule to keep so I didn’t. 🙂

        • I make quiche freezer meals all the time. The secret is to make everything but the eggs and freeze it. They I just crack the eggs fresh and bake it. It still takes a little time, but it means I can chop and shred tons of veggies and cheese at once.

          I’ve also frozen fritattas (very similar ingredients) with raw eggs and baked them when I take them out and they are just as good as “fresh” , but it can be a bit tricky freezing the liquid egg.

      • Hi Heather; 1 • I loved this cupcake recipe, because it does not contain flour, in the end it is an omelette served in the shape of a cupcake, perfect for brunch, very good. These hot days I resist turning on the oven, so I think , which will be very good, made in a saucepan with a grid at the base and the cakes on top, covered and cooked slowly as if it were an oven 2 • You cannot imagine how grateful you are if you focus on the recipe without a prior will; I will never understand, pastry chef to your cakes, really, it is appreciated. Best regards from Spain and take care about your self. Kisses

  1. 5 stars
    Do you have any posts regarding freezer meals for postpartum? Having baby 4 in 2 weeks and really need some healthy go to’s!

  2. 5 stars
    These are absolutely delicious! I made the mozzarella, cherry tomato and baby spinach ones this morning. And I plan on making bacon and cheddar another time – basically a pastryless quiche lorraine! However, my muffins stuck to the paper and I just can’t seem to avoid that! I lost a lot of muffin by peeling the cupcake liner off. Any tips?