Healthy Egg Muffins (3 Easy Ways)

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Start the day the right way with these healthy egg muffins – a simple mixture of eggs and your choice of vegetables, cheese, and herbs baked into tasty mini frittatas! These muffins are a great grab-and-go breakfast and healthy snack. Three flavor ideas included!

Want more eggylicious recipes? Try these Viral Pesto Eggs and this Breakfast Frittata Sandwich!

You know what they say: “breakfast is the most important meal of the day,” so I love trying new ways to incorporate nutrient-dense, balanced breakfasts into my routine. These healthy veggie egg muffins are quick, simple, and great on the go.

The best part? There’s no such thing as food boredom with this healthy egg muffin recipe in your meal prep rotation. You can choose from one of my three favorite combinations of nourishing mix-ins or use the egg base as a blank canvas and make these egg breakfast muffins your own.

While you’re here, check out more of my favorite breakfast meal prep recipes for busy mornings. Now let’s make the best egg muffins in three different flavors!

Ingredients You’ll Need

For the base recipe, you’ll need these simple ingredients.

  • Extra-virgin olive oil: You’ll need a neutral oil to coat the muffin pan and prevent the egg base from sticking. You can also use avocado oil.
  • Eggs: Eggs are a great source of lean protein. You’ll need a half dozen large eggs to make 6 to 8 egg cups (depending on the size of your muffin tin).
  • Milk (optional): It’s not necessary, but adding milk makes the egg muffins fluffy and puff up more. Try it!
  • Salt and pepper (to taste): To enhance the naturally smooth and buttery egg flavor.

For additional mix-ins, see “recipe variations” further down the page.

Ingredients to make breakfast egg muffins on the table.

How To Make

  1. Choose your flavor: First, choose the ingredients you want to use and prep the veggies.
  2. Prepare for baking: Then, preheat your oven to 400F (200C) and coat a muffin pan with extra virgin olive oil (or silicone liners). Set aside.
Preparing the pan for making egg muffins.
  1. Mix egg base: Meanwhile, make the egg base. Crack the eggs into a large bowl and then add the milk (if using) and salt and pepper. Whisk until the eggs are light and fluffy.

Feta, cherry tomato & basil:

  • Chop mix-ins: Cut the cherry tomatoes in half and roughly chop the basil leaves.
  • Mix: Add 4 tomato halves, fresh basil, crumbled feta, and spring onions to each cup.

Mushroom, parsley & parmesan

  • Chop and cook mushrooms: Chop the mushrooms. Heat extra virgin olive oil in a pan on medium heat, and then add the chopped mushrooms. Season to taste with salt and pepper and cook for 5 minutes. Add the chopped parsley and remove the pan from the heat.
  • Fill: Divide the cooked mushroom evenly between the muffin cups along with the parmesan.
mushroom and spinach cooking in a pan

Bell pepper, sun-dried tomato & spinach

  • Cook bell pepper: Heat oil in a pan over medium heat. Add chopped red peppers and cook for 5 minutes, seasoning with salt and pepper.
  • Add spinach: Add the fresh spinach and let it wilt for a couple of minutes. Then, mix in chopped sun-dried tomatoes.
Chopped veggies for making healthy egg muffins.
  1. Add mix-ins: Divide your toppings and mix-ins evenly between each muffin tin, and then pour the egg mixture over the top until the cups are 3/4 full.
  1. Bake: Transfer to your preheated oven and bake until firm and golden on top (15 to 20 minutes). Remove from the oven and let cool for 5 to 10 minutes before taking them off the pan.
Egg muffins baked in the pan ready to serve.

These 3 variations are just some ideas!

I love breakfast muffins because you can pretty much use any leftover veggies to make a delicious breakfast.

Feel free to use your favorite veggies, cheese (cheddar cheese and goat cheese work great), and lots of fresh herbs for extra flavor to bring these baked egg muffins to the next level!

How to Store

Storing: To store, let them cool completely. Then, transfer them to an airtight container (or single-serving resealable bags) and refrigerate them for up to 4 days. They can also be wrapped individually in some parchment paper and frozen for up to 3 months.

Reheating: To reheat, place them on a microwave-safe plate wrapped in a paper towel and microwave for 30 seconds to a minute (until the center is heated through) – 1 to 2 minutes if frozen.

These healthy egg muffin cups are delicious eaten warm or at room temperature.

Don’t forget to check out this incredible Beginner’s Meal Prep Guide: to Stress-Free Cooking!

Stack of breakfast egg muffins with one cut in half to show inside.

Tips

Grease your muffin tin WELL: A layer of oil between the egg mixture and the tin will prevent the muffins from sticking, so don’t forget to generously coat your muffin pan with oil.

Silicone muffin pan/liners: If you happen to have a silicone muffin pan, be sure to grease that as well. You can also use liners or parchment paper to line the muffin cups.

Overhead of all the egg muffins on a plate to show different variations.

F.A.Q.

Can I make healthy egg muffins with all egg whites?

I don’t recommend using all egg whites. The muffins need some fat from the egg yolks to stay soft and moist. Using all egg whites may result in chewy, spongey egg muffins. If you want to incorporate egg whites, I recommend using whole eggs and egg whites equally.

Do you need to spray silicone muffin cups?

It depends on what you’re making, but for egg muffins, yes – you should coat silicone muffin cups with oil so they pop right out of the molds when they’re ready.

Hand holding an egg muffin up over the others.

Why I Love This Recipe

  • Great on-the-go protein-packed breakfast and healthy snack.
  • Vegetarian, gluten-free, and can easily be made without any cheese or dairy.
  • Easy to customize with different veggies, cheeses, and flavors.
  • Great healthy make-ahead breakfast – make one batch for now and freeze a batch for later.

Other Healthy Quick Breakfasts You’ll Love

And for more meal prep breakfasts, check out these 25 easy breakfast recipes.

If you try this healthy egg muffins recipe, please leave a comment and a rating and let me know how much you liked it!

Healthy Egg Muffins (3 Easy Ways)

Start the day the right way with these healthy egg muffins – a simple mixture of eggs and your choice of vegetables, cheeses, and herbs baked into tasty mini frittatas! These muffins are a great grab-and-go breakfast and healthy snack. Three flavor ideas included!
Prep Time10 minutes
Cook Time20 minutes
Total Time30 minutes
Course: Breakfast
Cuisine: Vegetarian
Servings: 6 muffins
Calories: 90kcal
Author: Sara Trezzi

Ingredients

Egg base

  • 1 tablespoon extra-virgin olive oil
  • 6 large eggs
  • ¼ cup milk - optional – you can substitute for any plant-based milk or omit it entirely
  • Salt and pepper to taste

Feta, Cherry Tomatoes & Basil (for 6 egg muffins)

  • ¼ cup crumbled feta
  • 12 cherry tomatoes
  • 12 basil leaves
  • 2 spring onions - finely sliced

Mushrooms, Parsley & Parmesan (for 6 egg muffins)

  • 1/2 tablespoon extra-virgin olive oil
  • 2 cups chestnut mushrooms
  • Salt and pepper
  • 3 tablespoons fresh parsley - chopped
  • ¼ cup grated parmesan

Bell Peppers, Sundried Tomatoes & Spinach (for 6 egg muffins)

  • 1/2 tablespoon extra-virgin olive oil
  • 1 bell pepper - chopped (I used ½ green and ½ red bell pepper)
  • Salt and pepper
  • 3 sundried tomatoes
  • 2 cups packed fresh baby spinach

Instructions

Egg base (same for all variations)

  • Preheat the oven to 400F (200C). Coat a muffin pan with extra-virgin olive oil. Or, you can use silicon liners too.
  • Crack the 6 eggs into a large bowl, add salt and pepper and the milk (if using it), and whisk until the eggs are airy and fluffy.

Feta, Cherry Tomatoes & Basil

  • Roughly chop the basil leaves, and cut in half the cherry tomatoes.
  • Add 4 cherry tomato halves to each muffin tray, and sprinkle with the chopped basil, crumbled feta, and spring onions.
  • Fill each muffin tray with the egg mix until they are ¾ full, and bake at 400F (200C) for 15-20 minutes until the egg muffins look golden on top. Remove the pan from the oven, let the muffins cool slightly, and then remove them from the pan.

Mushrooms, Parsley & Parmesan

  • Chop the mushrooms. Heat a pan on medium heat, add the extra-virgin olive oil, add the mushrooms, salt, and pepper to taste, and let them cook for 5 minutes. Add the chopped parsley, and remove it from the heath.
  • Divide the mushrooms evenly into the muffin tray, add the parmesan, and fill each muffin cup with the egg mix until they are ¾ full and bake at 400F (200C) for 15-20 minutes until the egg muffins look golden on top. Remove the pan from the oven, let the muffins cool slightly, and then remove them from the pan.

Bell Peppers, Sundried Tomatoes & Spinach

  • Heat a pan on medium heat, add the extra-virgin olive oil, add the chopped bell peppers, salt, and pepper to taste, and let them cook for 5 minutes. Add the baby spinach, and let them wilt for a couple of minutes. Chop the sundried tomatoes, and mix them in.
  • Divide the mixture evenly into the muffin tray.
  • Fill each muffin cup with the egg mix until they are ¾ full, and bake at 400F (200C) for 15-20 minutes until the egg muffins look golden on top. Remove the pan from the oven, let the muffins cool slightly, and then remove them from the pan.

Notes

Note 1: These healthy egg muffin cups are delicious eaten warm or at room temperature.
Note 2: Grease your muffin tin WELL to prevent the muffins from sticking.
How to Store: Let the muffins cool completely. Then, transfer them to an airtight container (or single-serving resealable bags) and refrigerate them for up to 4 days. Egg muffins can also be wrapped individually and frozen for up to 3 months.
To reheat your egg muffins, place them on a microwave-safe plate wrapped in a paper towel and microwave for 30 seconds to a minute ( until the center is heated through)—1 to 2 minutes from frozen.
*Nutrition information is a rough estimate per serving of the basic egg muffin recipe.

Nutrition

Calories: 90kcal | Carbohydrates: 1g | Protein: 6g | Fat: 7g | Sugar: 1g

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2 Comments

  1. I used 1 red capsicum, half an onion, a handful of shallots and 10 cherry tomatoes, and 9 eggs. I forgot to fry the capsicum beforehand but it turned out great! I also used a regular sized muffin tin and it made 18 egg muffins for me. I also had to bake mine for about 24 minutes. these are so yummy and easy for meal prep! thank you again!

    1. Thank you, KA! Great alternative ingredients 🙂