Breakfast Egg Muffins Recipe (Egg Cups)

Name: Breakfast Egg Muffins Recipe (Egg Cups)
Prep time: 15 min
Cook time: 30 min
Total time: 45 min
Ingredients: 4 slices bacon (diced); 1 cup onion (finely chopped); 1 tsp minced garlic; 1 cup finely diced vegetables (Spinach, bell pepper, broccoli, zucchini, tomatoes, etc.); 12 eggs (beaten); 1 tsp Dijon mustard; ½ tsp sea salt; ¼ tsp pepper; ¼ tsp paprika; 1 cup shredded cheddar cheese

By Laura

Posted May 01, 2021, Updated Aug 12, 2023

5 from 11 votes

4 Comments

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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!

overhead photo of 6 Breakfast Egg Muffins (Egg Cups)

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.

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 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 TBS 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.

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!

Fill a muffin tin & 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.

Serve

If you’re wondering to serve with these egg muffins, whether you eat them for breakfast, lunch or a snack, here are some great suggestions for you!

For breakfast I like serving savory and sweet options together – try our Greek yogurt pancakes, these cinnamon rolls, banana bread, french toast, waffles, and so many more breakfast recipes. Here’s a great roundup of all the healthy breakfast ideas on my site!
Serve with a side of these crispy oven roasted potatoes!
Make this no knead bread for a crusty comforting side dish.
Didn’t prepare bread 24 hours in advance? No problem! Make these dinner rolls or this pretzel bread!
I know there’s already yummy veggies in these breakfast egg muffins, but I love serving them with roasted broccoli, Brussels sprouts, roasted beets, roasted green beans, etc.
Serve this egg muffin recipe with some roasted potatoes, hash browns, or roasted sweet potatoes!

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

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.

More egg recipes

Try this frittata recipe – ready in 20 minutes!
This egg bake is a great make-ahead meal to bake the night before and warm in the morning.
Who doesn’t love egg salad? This recipe is the best!
Try our hash brown crusted quiche or crustless quiche (both gluten-free)!

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

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