Low Calorie Healthy Egg Muffins (Mini Omelets)

10 Best Egg Muffins for Breakfast

These 5 Low Calorie Egg Muffins for Breakfast are healthy and easy to make. From vegetarian options, to bacon muffin cup eggs, or egg muffins with sausage, there are lots of yummy combinations to try! Best of all, these healthy baked omelets start at just 36 calories!

10 Best Egg Muffins for Breakfast

Everything You’ll Need

Low Calorie Healthy Egg Muffins

Low Calorie Egg Bites Recipe Variations

Low Sodium Egg Muffins

To reduce the sodium in these mini omelets, remove the salt from the recipe and choose low sodium cheese, and low sodium add ins. The first recipe (the Goat Cheese Omelet) is your best bet as the others have salty meats, and salty ingredients in them.

High Protein Egg Muffins

These mini omelets are already very high in protein, you can in some Healthy Breakfast Sausage to your omelets to boost protein even more.

Low Carb Egg Muffins

These egg muffins are already very low in carbs! You can boost protein more as noted above to balance them out more.

Low Sugar Egg Muffins

Thanks to the healthy nature of these egg muffins, they are already low in sugar. You can boost the protein more to balance out the meal should you like. But these have less than 1g of sugar each.

Vegetarian Egg Muffins

Choose the Greek Veggie, and Goat Cheese omelets below. Both are already vegetarian.

Dairy Free Egg Muffins

Feel free to remove the cheese from the recipe, or swap with vegan cheese. I like to do this with the Greek muffin cups below. With all the yummy ingredients you won’t miss the cheese.

10 Best Egg Muffins for Breakfast

Healthy Egg Muffins Cups Meal Prep and Storage

Meal Prep

  1. Prep – Prepare and bake the mini omelets as directed.
  2. Cover – Move to a gallon freezer bag or lined container.
  3. Refrigerate or Freeze – Will hold for 4 days in the fridge. And in the freezer for 1 month. 
  4. Cook – Wrap in a damp paper towels and microwave 2 minutes for defrosted, or 3-4 minutes for frozen.

Leftover Storage

  • Cook – Cook as directed below.
  • Individual or Family Servings – Add one slice to a container for single serve. Or as many servings as you need for the full family for family servings. Cover and store for later. 
  • Refrigerate or Freeze – Will hold for 4 days in the fridge. And in the freezer for 1 month. 
  • Reheat – Wrap in a damp paper towels and microwave 2 minutes for defrosted, or 3-4 minutes for frozen.
10 Best Egg Muffins for Breakfast

Low Calorie Healthy Egg Muffins (Mini Omelets)

10 Best Egg Muffins for Breakfast

Low Calorie Egg Muffin Cup Omelet

Lose Weight By Eating
These 5 egg muffins recipes are easy to make and packed full of protein and healthy ingredients.
The first recipe for baked omelets in muffin cups comes from our best selling cookbook (see photo below). Readers loved this recipe so much, that we added 4 more options to try.
Special Tip: Try adding a few dashes of hot sauce to the eggs before whisking for a kick of flavor and heat.
5 from 1 vote
Prep Time 5 minutes
Cook Time 20 minutes
Resting Time: 5 minutes
Total Time 30 minutes
Course Breakfast
Cuisine American, French
Servings 12 servings
Calories 36 kcal



Cheddar Bacon Egg Muffins:

Ham and Cheese Egg Muffins:


  • Preheat the oven to 350°F.
  • Spray a 12-cup muffin pan with oil spray.
  • Divide the veggies and protein among the muffin cups.
  • In a large bowl, whisk together the eggs, egg whites, salt, and pepper.
  • Pour 2 tablespoons of the egg mixture into each muffin cup, then top each with 1 teaspoon of cheese.
  • Bake the omelets for 20 minutes, then let them rest for 5 minutes in the pan (this will help them stay together).



detox week


Serving: 1omeletCalories: 36kcalCarbohydrates: 1gProtein: 3.5gFat: 2.1gSaturated Fat: 0.7gCholesterol: 64mgSodium: 139mgPotassium: 63mgFiber: 0.2gSugar: 0.7gCalcium: 13mgIron: 0mg
Keyword Healthy Egg Muffin Cup Omelet, Healthy Egg Muffin Cups, Low Calorie Egg Muffin Cup Omelet, Low Calorie Egg Muffin Cups
Tried this recipe?Let us know how it was!

About the Author

Hi, my name is Audrey Johns and I am a 4 time best selling cookbook author! All 4 of my low calorie cookbooks are published by HarperCollins (the oldest publishing house in the US!) and have been featured on prominent TV shows like The Today Show, Rachael Ray and The Doctors. I am a low calorie and healthy recipe authority and my delicious recipes are tried and loved by thousands of readers. 

After a one year 150 pound weight loss (and I’ve kept it off for 13 years!) I started sharing all of my low calorie recipes with the world. They are always all-natural and geared around weight loss and weight management. I have even made some of these recipes with my Biggest Loser pal Bob Harper! Check out my weight loss story, my best selling cookbooks, and my numerous TV appearances by clicking here.

Nutrition and Calories in Egg Bites

The nutrition label below is based off the first recipe (Goat Cheese Veggie Egg Muffins). It reflects one serving, which is one egg muffin cup.

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egg muffins for breakfast

Article History:

  • Originally written and published January 2, 2018 by Audrey Johns
  • Most recent update on November 12, 2023 by Audrey Johns

1 thought on “Low Calorie Healthy Egg Muffins (Mini Omelets)”

  1. Pingback: Low Calorie Chaffle Recipe {JUST 53 CALORIES} - Lose Weight By Eating

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