Breakfast Egg Muffins Recipe (Egg Cups)

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This egg muffins recipe is a delicious, healthy, low-carb, make-ahead breakfast that’s freezer-friendly. Egg cups are easy to make with only 8 ingredients (including eggs, veggies, cheese, and spices) and are customizable! 

two egg muffins on a plate


These egg muffs are a delicious healthy breakfast recipe that’s perfect for meal prep (just like these breakfast egg sandwiches)! This simple, straightforward egg muffin recipe is made with with bacon, eggs, vegetables and cheese.

No extras (like milk, bread, potatoes, etc.). Just a bunch of protein and nutrients to start the day right! 

Because eggs are so healthy and versatile they can be enjoyed for breakfast lunch and dinner! We often make egg muffins, egg casserole, this amazing omelette recipe, and this homemade frittata for healthy meals.

overhead photo of 6 Breakfast Egg Muffins (Egg Cups)

Egg Muffins: Ingredients & Substitutions

These egg muffins are highly customizable to your specific tastes! Here are some notes about the ingredients. 

overhead view of the labeled ingredients in this Breakfast Egg Muffins Recipe (Egg Cups)
  • Bacon. Turkey bacon can be used in place of regular bacon. However, because of the lower fat content, you will need to add 1 Tablespoon olive oil to the fry pan when you add the veggies to cook them well.  You can also use crumbled breakfast sausage in place of bacon with equally delicious results! If you wish to leave out the bacon and make this vegetarian, use 2 TBS olive oil to sauté the vegetables.
  • Minced Garlic. Garlic powder can be used in place of minced garlic, just add it with the rest of the spices. 
  • Onion. I usually use a sweet, white onion. Any variety works well: red onion, yellow onion, green onions, etc. 
  • Vegetables. Choose your favorite veggies! Bell peppers, broccoli, shredded zucchini, carrots, etc. 
  • Dijon mustard. Any mustard variety works well in these egg muffins! 
  • Eggs. there is no substituions for eggs in these breakfast egg cups. 
  • Cheddar Cheese. I recommend an extra sharp cheddar cheese for the best flavor! Other cheeses that taste great in this egg muffin recipe are: Colby jack, Swiss cheese, pepper jack (for a spicy flavor) and mozzarella! 

How to Make Egg Muffins

This egg muffin recipe is really easy to make, as always we’ll walk through the process step by step, and don’t forget to watch the video! 

Cook the bacon, onion and garlic

The first step in making these egg muffin cups is to sauté the bacon, onion and garlic over medium heat until the bacon just begins to brown. Be sure to stir every few minutes. 

Note: For a vegetarian version (without bacon), simply add 2 TBS olive oil to the pan and sauté the onions and garlic together until the onions are soft, then add the rest of the veggies! 

two overhead photos showing How to Make Breakfast Egg Muffins (Egg Cups)

Add veggies, cover and cook

Once the bacon just begins to brown, add vegetables, cover and cook for 5-10 minutes or until the veggies are soft and bacon is browned, stirring occasionally.

Note: If you use a variety of vegetables that cook at different speeds, make sure to handle that accordingly. For example, carrots cook faster than zucchini, so I would add the carrots and cook them until they become soft, then add zucchini. 

Cool

Remove the pan from the heat and let the veggie/bacon mixture cool while you finish making the egg muffins recipe.  

two overhead photos showing How to Make Breakfast Egg Muffins (Egg Cups)

Combine Eggs & Spices

While the bacon/veggie mixture is cooling, whisk the eggs. Then add mustard, salt, pepper and paprika to the beaten eggs and whisk to combine. 

Next, add the cooled bacon/veggie mixture to the beaten eggs and stir until the mixture is uniform throughout. Then add the cheese!

two overhead photos showing How to Make Breakfast Egg Muffins (Egg Cups)

Bake

Fill each well of the prepared muffin tin ¾ full with egg mixture. Be careful not overfill the wells, because these egg muffins rise and will overflow if they are filled too much!

Bake in preheated oven for 25-30 minutes, or until tops are set and slightly browned and spring back when lightly pressed. 

Cool

Let the egg cups cool for 5 minutes, then release them from the pan using a spoon or sharp knife, and serve warm.

two overhead photos showing How to Make Breakfast Egg Muffins (Egg Cups)

Serve

Serve these egg muffins with your favorite breakfast recipes, I especially love serving them with crispy potatoes and fruit salad. Or, if serving for dinner a nice side salad goes very well with egg muffins!

overhead view of 6 Breakfast Egg Muffins (Egg Cups) on a cooling rack

Egg Cups Recipe FAQs

How do you store egg muffins?

Store these egg muffins in an airtight container in the refrigerator for up to 5 days,

How do you freeze egg muffins?

To freeze, simply place the egg muffins in a freezer-friendly, airtight container and freeze for up to 2 months. To thaw, transfer the egg muffins to the refrigerator and let thaw overnight. Or reheat in the microwave for 60 seconds per muffin. 

How do you keep egg muffins from collapsing in the middle?

Follow this egg muffin recipe and you won’t have any sinking middles! Make sure you don’t over-whisk the ingredients, which creates air bubbles that could cause sinking.

Will egg muffins stick to paper liners?

In my experience, yes. That’s why I recommend greasing your muffin in well. They bake up nice and hearty so they are easy to remove if the pan is properly greased.

two Breakfast Egg Muffins on a plate, one cut in half

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Breakfast Egg Muffins Recipe (Egg Cups)

Laura
This egg muffins recipe is a delicious, healthy, low-carb, make-ahead breakfast that's freezer-friendly. Egg cups are easy to make with only 8 ingredients (including eggs, veggies, cheese, and spices) and are customizable!
5 from 16 votes
Course Breakfast, brunch, lunch, Main Course
Cuisine American
Servings 14 Muffins
Calories 119
Prep Time15 minutes
Cook Time30 minutes
Total Time45 minutes

Ingredients 
 

Instructions 

  • Preheat oven to 350 degrees F. Grease a standard 12-cup muffin tin, set aside.
  • In a large skillet, over medium heat, cook diced bacon until it just starts becomes soft.
  • Add minced garlic and onion and cook until bacon begins to brown.
  • Add vegetables, cover and cook for 5-10 minutes or until the veggies are soft and bacon is browned, stirring occasionally.
  • Remove from heat and let cool.
  • In a medium bowl, whisk together eggs.
  • Add mustard, sea salt, pepper and paprika and whisk to combine.
  • Add cooled bacon/veggie mixture to the beaten eggs and stir to combine.
  • Add cheese. Stir to combine.
  • Fill each well of the prepared muffin tin ¾ full with egg mixture. Do not overfill! These egg muffins rise and will overflow if the wells are filled too much!
  • Bake in preheated oven for 25-30 minutes, or until tops are set and slightly browned.
  • Cool for 5 minutes and serve warm.

Video

Notes

Ingredient Substitutions
  • Bacon. Turkey bacon can be used in place of regular bacon. However, because of the lower fat content, add 1 Tablespoon olive oil to the fry pan when you add the veggies to cook them well.  You can also use crumbled breakfast sausage in place of bacon with equally delicious results! If you wish to leave out the bacon and make this vegetarian, use 2 Tablespoons olive oil to sauté the vegetables.
  • Minced Garlic. Garlic powder can be used in place of minced garlic, just add it with the rest of the spices. 
  • Onion. I usually use a sweet, white onion. Any variety works well: red onion, yellow onion, green onions, etc. 
  • Vegetables. Choose your favorite veggies! Bell peppers, broccoli, shredded zucchini, carrots, etc. 
  • Dijon mustard. Any mustard variety works well in these egg muffins! 
  • Eggs. there is no substituions for eggs in these breakfast egg cups. 
  • Cheddar Cheese. I recommend an extra sharp cheddar cheese for the best flavor! Other cheeses that taste great in this egg muffin recipe are: Colby jack, Swiss cheese, pepper jack (for a spicy flavor) and mozzarella! 
Store/Freeze
Store these egg muffins in an airtight container in the refrigerator for up to 5 days, or in the freezer for up to 2 months.
To freeze, simply place the egg muffins in a freezer-friendly, airtight container and freeze for up to 2 months. To thaw, transfer the egg muffins to the refrigerator and let thaw overnight. Or reheat in the microwave for 60 seconds per muffin. 

Nutrition

Serving: 1muffin | Calories: 119kcal | Carbohydrates: 2g | Protein: 8g | Fat: 9g | Saturated Fat: 4g | Trans Fat: 1g | Cholesterol: 153mg | Sodium: 233mg | Potassium: 102mg | Fiber: 1g | Sugar: 1g | Vitamin A: 325IU | Vitamin C: 5mg | Calcium: 84mg | Iron: 1mg

Nutrition information is automatically calculated, so should only be used as an approximation.

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8 Comments

  1. 5 stars
    Made these last night to prep for the week and they are DELICIOUS! Did add some other seasonings and made them with turkey bacon, red peppers, onions and spinach. My partner and I are definitely adding this to the weekly meal prep list now! Thank you!!

  2. 5 stars
    Made these this morning, misread the instructions and only used 4 eggs. It made 7 egg muffins and they’re great thanks!

  3. 5 stars
    My husband & I love this recipe! As you said, I add my own spices & such, but the base recipe works great. We have this for Sunday breakfast, & then my husband has 1 “muffin” for breakfast at work every day during the week.