It’s easy to make delicious Egg Muffins with your choice of fillings, including veggies, meat or cheese. Meal prep the muffins for an on-the-go breakfast during the week. They’re healthy, gluten free and at ZERO net carbs per muffin, they’re perfect for those on a keto diet!

egg muffins on white plate

If you’re looking for a tasty, easy and healthy breakfast for meal prepping, then you’ve come to the right place. These egg muffins are easily made in muffin tins in just 30 minutes!

You can mix up the fillings with the ingredients of your choice. Some of my favorite combos include bacon and pepper jack cheese, cherry tomatoes and mozzarella, and bell pepper and cheddar.

These muffins are perfect for everyone. Meal prepping breakfast for one person for the week? Mix up a batch for yourself!

Planning breakfast for the week for your family? Get the kids involved and let them add the fillings of their choice. It’s easy to mix and match the fillings, or make them all the same. These breakfast egg muffins are extremely versatile and healthy!

Made without any fillings, these egg muffins are naturally gluten free, vegetarian and only 57 calories per muffin, not to mention they only contain 1 total carb and ZERO net carbs! Adding fillings will adjust these numbers slightly, but you’ll still end up with a low calorie, low carb breakfast, that everyone will love!

Serve them as a grab-and-go breakfast when heading to school or work, or as a quick and easy afternoon snack. You can also make a triple batch and serve them at a brunch party along with my famous Bagel Bar. Just call them mini frittatas and everyone at your brunch will think they’re super fancy! We’ll just make it our little secret that they’re healthy and easy to make!

ingredients for egg muffins

Ingredients you’ll need

You only need 5 basic ingredients to make the base for these egg muffins.

  • Large eggs – if you’re using extra large eggs, I recommend cutting the recipe down from 10 eggs, to 8 eggs.
  • Milk – I used 2% milk in this recipe, but feel free to use whole milk or almond milk in it’s place.
  • Garlic powder
  • Salt
  • Black pepper

Filling options

The options really are endless when it comes to the filling options for these muffins. If you’re making one filling for all 12 muffins, you’ll need approximately 2 1/4 cups of the filling.

I’ve included measurements below for making one batch of the muffins with the various filling combinations. Feel free to cut the ingredient amounts in half to make two different flavors of muffins.

  • Cheddar pepper: 1 cup diced bell pepper + 1/4 cup diced green onions + 1 cup shredded cheddar cheese
  • Caprese: 1 cup halved cherry tomatoes + 1/4 cup fresh chopped basil (or 1 tablespoon dried basil) + 1 cup shredded mozzarella cheese
  • Mediterranean: 1 cup julienned sun dried tomatoes + 1/4 cup fresh chopped spinach + 1 cup crumbled feta cheese
  • Spicy bacon: 1 cup cooked, chopped bacon + 1/4 cup minced jalapenos + 1 cup shredded pepper jack cheese
  • The Denver omelette: 1/2 cup diced ham + 1/2 cup diced onions + 1/2 cup diced bell pepper + 1 cup shredded cheddar cheese
collage of images showing how to make egg muffins

Step by step instructions

  1. Whisk the eggs, milk, garlic powder, salt and pepper together in a medium mixing bowl.
  2. Combine the fillings of your choice.
  3. Spray a non-stick muffin tin with cooking spray. Add the fillings to the muffin tin, filling them about halfway full.
  4. Pour the egg mixture into the muffin tins, either using a container with a spout for pouring, or using a ladle with a spout. Fill the muffin tins almost all of the way full, but they should not easily spill out when transferring them to the oven.
  5. Bake the egg muffins for 20 minutes. The eggs will puff up while baking, don’t be alarmed, that’s totally normal!
  6. Remove the egg muffins from the oven and allow them to cool for 10 minutes. Use a small knife around the edges to remove the egg muffins from the muffin tin.

The egg muffins can be eaten immediately or stored in the refrigerator for up to 5 days.

egg muffin cut in half on white plate

Topping ideas

Want to take these egg muffins to the next level? Throw on some toppings! Here are a few ideas to get you started.

  • Hot sauce – we’re big fans of pico pica at our house and I love drizzling it over the spicy bacon egg muffins!
  • Creamy chipotle sauce – whenever I have this on hand in my refrigerator, I pretty much drizzle it on everything in sight! It’s delicious on the cheddar pepper muffins!
  • Salsa – pop a spoonful of your favorite salsa on top of the muffins for extra spice and flavor!
  • Avocado – slices of creamy avocado are delicious on any of the muffin flavors!
  • Everything bagel seasoning – why not combine everyone’s favorite breakfast seasoning with these flavorful breakfast muffins!
  • Herbs – for a bright, fresh flavor, feel free to top the muffins with fresh chopped cilantro, basil or green onions.
collage of images showing how to make egg muffins with paper liners

Should you use paper liners?

I have tested this recipe using paper liners and pouring directly into the muffin tin. I’ve also tried making them in a metal muffin tin, as well as a stoneware muffin pan.

I actually prefer the texture when the muffins are baked in the stoneware pan, but since I know that most people don’t own a stoneware pan, I’m going to give you the two tricks I used to emulate the texture in a metal muffin tin.

  1. Use paper liners and spray the inside of the liners with cooking spray. If you do not spray the paper liners, they will stick to the egg muffins and you’ll be sitting there peeling liner off of your muffins for 10 minutes. No one wants that!
  2. Set the metal muffin tin on a baking sheet before placing it in the oven. This will prevent the bottom of the egg muffins from becoming brown.

If you’re okay with a little brown around the edges and bottom of the muffins, feel free to pour the egg mixture directly into the muffin tins to make the muffins.

Nutritional information

The base of the egg muffins is vegetarian and gluten free. Each egg muffin, without the optional fillings, contains 57 calories and 0 net carbs. I’ve also calculated the nutritional information for each egg muffin, with the different filling options that I’ve provided.

If you’re looking for the lowest calorie option, the caprese is for you at 88 calories per muffin. If you’re looking for the lowest carb option, the spicy bacon or caprese are perfect for you at 0 net carbs and 1 total carb per muffin.

  • Cheddar pepper: 100 calories, 1 net carb, 2 total carbs, vegetarian and gluten free.
  • Caprese: 88 calories, 0 net carbs, 1 total carb, vegetarian and gluten free.
  • Mediterranean: 114 calories, 5 net carbs, 6 total carbs, vegetarian and gluten free.
  • Spicy bacon: 175 calories, 0 net carbs, 1 total carb and gluten free.
  • The Denver omelette: 114 calories, 1 net carb, 2 total carbs and gluten free.
egg muffin on plate with bite taken out of it

Tips and tricks

  • Always be sure to generously spray cooking spray into the muffin tin, or paper liners before adding the filling. This will ensure the egg muffins come out of the tin easily and will make clean up a breeze!
  • The egg muffins will stay good in the refrigerator stored in an airtight container for up to 5 days. To reheat the muffins, wrap them in a damp paper towel and microwave for 15-20 seconds. This will keep them moist.
  • You can freeze the egg muffins for up to 3 months. Once the egg muffins have cooled completely, wrap each one in a piece of plastic wrap, then add all of them to a large freezer-safe zipper bag. To reheat frozen egg muffins, unwrap them from the plastic, wrap them in a damp paper towel and microwave for 60 seconds, or until warm.
  • You can make these egg muffins whole30 approved, by swapping traditional dairy milk with almond milk. No cheese can be added to the filling, but you can add bacon and veggies.
  • This recipe can easily be doubled or tripled. To adjust the serving size, simply hover over the “servings” in the recipe card below and adjust it from 12 to 24, or up to 36. The ingredient amounts will automatically update to the new serving size.
egg muffins on white plate with fork

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Egg Muffins

It's easy to make delicious Egg Muffins with your choice of fillings, including veggies, meat or cheese. Meal prep the muffins for an on-the-go breakfast during the week!

Ingredients

  • 10 large eggs
  • cup milk
  • ½ teaspoon garlic powder
  • 1 teaspoon salt
  • ½ teaspoon black pepper

Instructions

  • Preheat the oven to 350°F.
  • Whisk the eggs, milk, garlic powder, salt and black pepper together in a medium bowl.
  • Combine the fillings of your choice. (See the notes below for various filling options.)
  • Spray a 12 capacity non-stick muffin tin generously with cooking spray, or line each cup with paper liners and spray the inside of the liners.
  • Place the optional additions of your choice in the bottom of each muffin tin, filling them about halfway full.
  • Pour the egg mixture  into the muffin tins, either using a container with a spout for pouring, or using a ladle with a spout. Fill the muffin tins almost all of the way full, but they should not easily spill out when transferring them to the oven.
  • Place in the oven and bake for 20 minutes.
  • Remove from the oven and allow to cool for 10 minutes.
  • Use a small knife around the edges to remove the egg muffins and serve immediately or store for up to 4 days in the refrigerator.

Notes

  • The nutritional information provided below is for the egg muffins without any fillings. Please find the calories and carbs for each of the filling options listed below.
  • Filling options:
    • Spicy bacon: 1 cup cooked, chopped bacon +¼ cup minced jalapenos + 1 cup shredded pepper jack cheese
      • Nutrition per egg muffin: 175 calories, 0 net carbs, 1 total carb
    • Mediterranean: 1 cup julienned sun dried tomatoes + ¼ cup chopped spinach + 1 cup crumbled feta cheese
      • Nutrition per egg muffin: 114 calories, 5 net carbs, 6 total carbs
    • Cheddar pepper: 1 cup diced bell pepper + ¼ cup diced green onions + 1 cup shredded cheddar cheese
      • Nutrition per egg muffin: 100 calories, 1 net carb, 2 total carbs
    • Caprese: 1 cup halved cherry tomatoes + ¼ cup chopped fresh basil (or 1 tablespoon dried basil) + 1 cup shredded mozzarella cheese
      • Nutrition per egg muffin: 88 calories, 0 net carbs, 1 total carb
    • The Denver omelette: 1/2 cup diced ham + 1/2 cup diced onions + 1/2 cup diced bell pepper + 1 cup shredded cheddar cheese
      • Nutrition per egg muffin: 114 calories, 1 net carb, 2 total carbs
  • This recipe can easily be doubled or tripled. To adjust the serving size, simply hover over the “servings” number above and adjust it from 12 to 24, or up to 36. The ingredient amounts will automatically update to the new serving size.
  • The egg muffins will stay good in the refrigerator stored in an airtight container for up to 5 days. To reheat the muffins, wrap them in a damp paper towel and microwave for 15-20 seconds. This will keep them moist.
  • You can freeze the egg muffins for up to 3 months. Once the egg muffins have cooled completely, wrap each one in a piece of plastic wrap, then add all of them to a large freezer-safe zipper bag. To reheat frozen egg muffins, unwrap them from the plastic, wrap them in a damp paper towel and microwave for 60 seconds, or until warm.
  • You can make these egg muffins whole30 approved, by swapping traditional dairy milk with almond milk. No cheese can be added to the filling, but you can add bacon and veggies.
  • To prevent browning on the bottom of the muffins, set the metal muffin tin on a baking sheet before placing it in the oven.

Nutrition Facts

Calories 57kcal (3%)Carbohydrates 1gProtein 5g (10%)Fat 4g (6%)Saturated Fat 1g (5%)Trans Fat 1gCholesterol 137mg (46%)Sodium 249mg (10%)Potassium 62mg (2%)Fiber 1g (4%)Sugar 1g (1%)Vitamin A 209mg (4%)Vitamin C 1mg (1%)Calcium 29mg (3%)Iron 1mg (6%)
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