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Start your day with easy and delicious breakfast egg muffins! Packed with veggies, protein, and cheese, these make-ahead egg cups are perfect for busy mornings, meal prep, or a grab-and-go snack. Freezer-friendly and customizable!

breakfast egg muffins on a plate

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There’s something so satisfying about having a batch of breakfast egg muffins ready to go for the week. In our house, they’re a weekday lifesaver—quick, protein-packed, and easy to grab on busy mornings.

These easy breakfast egg muffins are super customizable. We mix in whatever we have on hand—cheese, spinach, ham, or veggies—and everyone gets their favorite combo. The kids love them, and I always sneak in extra greens when I can.

If you’re looking for a simple, make-ahead breakfast that’s both nourishing and convenient, this egg muffin recipe is it. You might also love these baked eggs, ham and cheese breakfast muffins, or this freezer-friendly breakfast burrito.

Why You Will Love This Healthy Breakfast Egg Muffins

  • Delicious and satisfying: This breakfast offers a flavorful combination of ingredients that’s sure to keep you satisfied throughout the morning.
  • Kids’ favorite: Kids love these cute and bite-sized muffins for breakfast.
  • Perfect for meal prep: I love that I can whip these up in minutes and make them ahead for busy mornings.
healthy breakfast muffins

Breakfast Egg Muffins Ingredients

For a full ingredients list with measurements, check the recipe card below.

ingredients for egg breakfast muffins
  • Vegetables: bell peppers, broccoli, carrot, onion.
  • Whole eggs: Use organic pasture-raised eggs for the best flavor of your egg muffins.
  • Cheese: I used cheddar cheese but you can use any cheese you prefer or you can omit the cheese for a dairy-free option.
  • Seasonings: a tsp of salt and a pinch of freshly ground black pepper. You can also add garlic powder or onion powder.
  • Bacon: It’s optional but it adds a lot of flavor.

How To Make Egg Muffins

sauteed vegetables in a skillet
  1. Sautee the vegetables. Saute peppers, shredded carrots, and onion in a large skillet over medium heat until tender.
whisked eggs in a bowl
  1. Whisk the eggs. In a large mixing bowl crack the eggs and lightly beat with a whisk. Season with salt and freshly ground black pepper.
mixing eggs, vegetables and bacon
  1. Mix eggs & veggies. Add sauteed vegetables to the whisked eggs, and stir. If you want you can also add some crumbled cooked bacon.
breakfast egg muffins in a muffin  pan
  1. Bake. Fill the muffin mold with egg mixture, top with cheese and bake in a preheated oven at 375 F for about 20 minutes.
egg breakfast muffins in muffin tin

Recipe Notes and Tips

  • Make sure you chop the vegetables into small and evenly sized pieces. Otherwise, the muffins might fall apart when you eat them.
  • Avoid moisture. Don’t add vegetables with a lot of water content like tomatoes or raw spinach. Make sure you first sautee any vegetables to prevent the egg muffins from becoming soggy.
  • Don’t over whisk the eggs for too long if you want light and fluffy egg muffins.
  • Fill the muffin cups only 3/4 otherwise, they can overflow while baking.
  • Let the cooked breakfast egg muffins cool for 5 minutes before you remove them from the muffin pan and serve them.
Breakfast Muffins

Flavor Variations

The possibilities for customizing your egg muffins are endless! I love mixing and matching by picking whatever protein, cheese, and vegetables I have on hand to create a variety of delicious flavor combinations.

  • Protein: you could use ham, ground chicken or turkey, breakfast sausage, chorizo, ground beef, and even ground venison.
  • Vegetables: other vegetables you could use are mushrooms and potatoes (Yukon Gold, Russet, or sweet potatoes).
  • Cheese: You could use crumbled feta, Parmesan cheese, Pepper Jack, Grueye, or your favorite cheese. 

Storing and Reheating Egg Muffins

These breakfast egg muffins are best fresh out of the oven – so if you can enjoy them right away, go for it! But they’re also great for meal prep. Just let them cool completely, then follow these simple storage and reheating tips:

  • Refrigerate: Store in an airtight container in the fridge for up to 5 days.
  • Freeze: Place in a freezer-safe container or wrapped in plastic wrap and bagged in a freezer-safe ziplock bag, and freeze for up to 3 months.
  • Thaw: Thaw frozen egg muffins in the fridge overnight.
  • Reheat: Pop them in the toaster oven for a couple of minutes to reheat.
holding a breakfast egg muffin

Recipe FAQs

Why are my egg muffins soggy?

Watery ingredients like tomatoes and raw vegetables like spinach, kale etc, can make the egg muffins soggy. If you want to use them, saute them first and drain as much liquid as possible.

More Easy Breakfast Ideas

If you are looking for more healthy and easy breakfast ideas, check out these recipes.

If you enjoyed this Breakfast Egg Muffins recipe or any other recipe on my blog, please leave a ⭐ star rating and let me know how it went in the 📝 comments below. Thanks for visiting!

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Breakfast Egg Muffins
5 from 16 votes

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Breakfast Egg Muffins

Start your day with easy and delicious breakfast egg muffins! Packed with veggies, protein, and cheese, these make-ahead egg cups are perfect for busy mornings, meal prep, or a grab-and-go snack. Freezer-friendly and customizable!
Prep Time: 10 minutes
Cook Time: 20 minutes
Total Time: 30 minutes
Servings: 12

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Ingredients 
 

Instructions 

  • Preheat oven to 375 F. Line a muffin tin with silicone baking cups or paper liners.
  • Saute peppers, shredded carrots, and onion in a skillet over medium heat until tender.
  • In a large mixing bowl crack the eggs and lightly beat with a whisk. (don’t overbeat them if you want to have fluffy egg muffins). Season with salt and freshly ground black pepper.
  • Add the sauteed vegetables and grated cheese to the whisked eggs, and toss to combine. If you want you can also add some crumbled cooked bacon.
  • Fill each muffin cup with the vegetable egg mixture so that it is filled to about 3/4 full. Be careful not to overfill the muffin cups. You can top each cup with about 1 Tbsp shredded cheese.
  • Bake in a preheated oven for about 20 minutes, or until the muffins are set and cooked through. They will puff in the oven but sink upon cooling. Allow the egg muffins to cool in the pan for about 5 minutes before removing.

Video

Notes

  • Make sure you chop the vegetables into small and evenly sized pieces. Otherwise, the muffins might fall apart when you eat them.
  • Avoid moisture. Don’t add vegetables with a lot of water content like tomatoes or raw spinach. Make sure you first sautee any vegetables to prevent the egg muffins from becoming soggy.
  • Don’t over whisk the eggs for too long if you want light and fluffy egg muffins.
  • Fill the muffin cups only 3/4 otherwise, they can overflow while baking.
  • Let the cooked breakfast egg muffins cool for 5 minutes before you remove them from the muffin pan and serve them.

Nutrition

Serving: 77g | Calories: 104kcal | Carbohydrates: 3g | Protein: 8g | Fat: 7g | Saturated Fat: 3g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 2g | Trans Fat: 0.02g | Cholesterol: 135mg | Sodium: 361mg | Potassium: 140mg | Fiber: 1g | Sugar: 1g | Vitamin A: 1460IU | Vitamin C: 20mg | Calcium: 77mg | Iron: 1mg

Nutrition Disclaimer: Nutritional values are estimates and may vary with ingredients, brands, and portion sizes. For accuracy, use your preferred nutrition calculator.

Like this recipe? Rate and comment below!

Disclaimer: The information provided in this recipe is for informational purposes only and should not be considered medical or nutritional advice. I am not a doctor or a dietitian. Always consult a qualified healthcare provider for personalized guidance regarding your diet or health. For more details, please read my full disclosure page.

 

About Neli Howard

Meet Neli Howard, the food blogger and recipe developer behind the food blog Delicious Meets Healthy. With over 12 years of cooking experience, Neli specializes in easy, wholesome recipes made with real ingredients and a lot of flavor. Her work has been featured in Forbes, MSN, Yahoo!, CNN, Healthline and more.

5 from 16 votes (1 rating without comment)

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28 Comments

  1. Debra Bartley says:

    5 stars
    Thank you for sharing this recipe

  2. Manjit Saundh says:

    Hi. It doesn’t day to sautée broccoli. Do you add them later?

    Thanks

    Manjit

    1. Neli | Delicious Meets Healthy says:

      yes, you add them with all vegetables

  3. Amber says:

    5 stars
    Delicious! Perfectly cooked

  4. Supriya Kutty says:

    5 stars
    Muffins were something that I tried for the very first time and I could not believe that it was made by me. Thank you so much for putting up this post as I was appreciated so much by my family.

  5. Ghei says:

    5 stars
    Tried it for the first time and it was delicious and so easy to make.

  6. Mary Hopkins says:

    Can I convert these muffins to make it a quiche for dinner? If so, would I need to add milk to the eggs in making the quiche?