Healthy Breakfast Egg Muffins {Freezable & Quick Go-Tos}

You’ll be glad you have these delicious, filling breakfast egg muffins during the morning rush or for a hangry afternoon snack.

These mini frittatas were game-changers when I became a new mom. You can freeze them and quickly reheat them in the microwave for a grab-and-go breakfast. 

How To Make the Best Breakfast Egg Muffins

Honestly, you can’t go wrong when it comes to making these delicious delights. I’ve made different variations of these over the years. Each time I make them I add something new or different. 

I first discovered egg muffins when I was pregnant with my son. While in pre-mom mode, I scoured the internet to find freezable meals to prepare for the first few weeks with a newborn. That’s when I found these egg muffins. They were my breakfast and snack time go-to’s for weeks.

I’ve also made these in preparation for traveling for work. All you need is a microwave to reheat and enjoy. 

serving egg muffins


When possible, purchase the highest quality eggs you can find. I prefer organic, pasture-raised eggs. If you have access to farm-fresh eggs or if you have your own chickens, take advantage. You’ll reap major benefits and so will nature.

When it comes to using the whole egg to egg white ratio, always use more whole eggs. Otherwise, the egg muffins will have more of a spongy texture. I prefer 8 whole eggs to 4 egg whites. 


mixing eggs


For the filling think veggies, protein, and cheese. 

I love my vegetables but I’ve found creating a good balance of egg to veggies is ideal. The intent is to fill each muffin cup with a healthy dose of vegetables without creating a salad muffin. 

The same thing applies when considering adding proteins such as turkey bacon. You don’t want to overdo it. Otherwise, the egg muffin won’t stick together. Furthermore, if you do decide to add turkey bacon or sausage, be sure to cook both before adding to the muffin cups.   

mixing filling


  1. Using each muffin cup as a guide the filling should make up about one-third to one-half.
  2. Another general rule of thumb is for every 12 eggs, use a total of 2 cups of finely chopped filling. 
  3. If using onions, protein, or cheese use only about 1/4-1/3 cup of each. 

Don’t worry though, I’ve got you covered. 


Depending on what you decide to use for the filling, your seasonings may vary. For example, if you add cheese and/or a salty protein like turkey bacon, you’ll want to add a little less salt to the eggs or completely omit. 

Here are some seasonings ideas to get you started:

  • Sea salt
  • Pepper
  • Garlic Powder
  • Basil
  • Italian Seasoning
  • Mrs. Dash Original
  • Tarragon
  • Parsley
  • Curry
  • Oregano

This list isn’t exhaustive but hopefully will give you a starting point. 


Do you have a favorite frittata you make or order at a restaurant? Think of what it contains. Consider using some of the following fillings:

  • Asparagus
  • Bell peppers
  • Broccoli
  • Cherry Tomatoes
  • Mushrooms (button or cremini work well)
  • Onions
  • Spinach
  • Turkey Bacon
  • Turkey Sausage
  • Parmesan, Mozzarella, or Feta Cheese

baked egg muffins


Below you’ll find three combinations you can try:

  1. Greek-style: Spinach, onions, feta cheese, and cherry tomatoes. 
  2. Peppered Up: Red, green, and yellow bell peppers, onion, and turkey sausage (or completely omit or substitute with spinach or asparagus).
  3. Veggie-style: Spinach, red bell pepper, onion, mushroom, and mozzarella (or omit the cheese).


You can mix the veggies and the filling with the eggs in one of two ways.

The main thing with either method is to ensure you fill the muffin cup up 3/4 of the way. The eggs will expand over the muffin pan while cooking but deflate quite a bit once out of the oven. 

  • Muffin Cup Method- Add your filling (veggies and protein) to the muffin pan cups filling about 1/3 to 1/2 of each cup.  Mix your eggs, seasoning, milk, and cheese in a bowl. Then pour into the muffin pan to fill 3/4 of the cup.  

filling in cups method

  • Bowl Method- If using 12 eggs, measure your filling to fit into 2 cups. Mix eggs, filling, seasonings, and milk in a bowl. Next, pour the egg mixture into the muffin pan again filling it 3/4 full.   

bowl mixing method

Personally, I’ve found both methods result in the same delicious egg muffin. However, with the muffin cup method, you’re a bit more in control of the ratio of filling within each cup. 

before baking


The best part of these muffins is not only the quickness and ease of making them but they also freeze well.

Once baked, allow the egg muffins to cool. Then place uncovered on a baking sheet in the freezer for 1-hour. This is known as a flash-freeze. 

Next you can individually wrap the egg muffins with plastic wrap and store in a glass container or in these Stasher silicone bags. If you prefer to use less plastic, store directly in a container or bag, without wrapping. 

Egg muffins will keep for about 3 months in the freezer or 3-4 days in the refrigerator. Simply reheat in the microwave and enjoy!

egg muffins

Healthy Breakfast Egg Muffins {Freezable & Quick Go-Tos}

Breakfast egg muffins make for a great breakfast or brunch dish. Combine your favorite veggies and proteins (if preferred) for a healthy filling in each cup. Breakfast egg muffins freeze wonderfully too.
Prep Time 10 minutes
Cook Time 20 minutes
Course Breakfast, Brunch
Cuisine American
Servings 12



  • 8 whole, organic eggs (pasture-raised)
  • 4 egg whites (organic, pasture-raised)


  • 1/4 cup yellow onion, chopped small (about 1/4 of an onion)
  • 1/2 cup organic, red bell pepper chopped small
  • 1/2 cup organic, green bell pepper chopped small
  • 1/2 cup organic, spinach chopped small
  • 1/4 cup mozzarella cheese, shredded


  • 3/4 teaspoon sea salt (I use Real Salt)
  • 1/2 teaspoon freshly ground black pepper
  • 1/2 teaspoon garlic powder
  • 1/2 teaspoon basil
  • 1/2 teaspoon oregano
  • 1/4 teaspoon tarragon


  • Preheat oven to 375°
  • Mix eggs, seasoning, and cheese in a bowl.
  • Evenly disburse bell peppers, spinach, and onions into each muffin cup. Fillling about 1/3 to 1/2 of the muffin cup.
  • Either spray muffin cups with oil or use muffin paper. Pour egg mixture into the muffin cups filling up to 3/4 of each cup.
  • Bake for 15-20 minutes until a tooth pick inserted comes out clean.


  • If using turkey bacon or sausage, be sure to cook before adding to the mixture. 
  • A general rule of thumb when it comes to filling is to use 2 cups of filling for every 12 eggs. Use between 1/4 cup to 1/3 cup of onions, cheese, and healthy protein each.
  • Be sure to chop your veggies small so you don't end up with big chunks.  
Keyword breakfast muffins, brunch ideas, egg muffins, eggs, healthy egg muffins

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