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Breakfast Egg Muffin Cups – 5 Healthy Variations

This Breakfast Egg Muffin Cups Recipe is a delicious make-ahead breakfast packed full of protein, veggies and is totally customizable! Make them ahead of time, refrigerate or freeze them, and then heat them for a quick breakfast.

a stack of breakfast egg muffin cups with mushrooms and tomato in the background

Breakfast Egg Muffins

I love to make breakfast meals that are filling, quick to make, pack in the nutrition and the leftovers store well! These breakfast egg cups fit every requirement! These egg cups are creamy, warm and perfectly portioned to be filling for kids and adults both!

Egg Muffin Cups 12 1

Ingredients for Breakfast Egg Cups

The ingredients for egg cups are very basic. The add-ins are really the star of the recipe and I have lots of variations for you to try. These are what you will need for the egg base:

  • Eggs – large eggs are best for this recipe
  • Milk – makes the egg cups more rich and a better texture. You can use any type of unsweetened milk
  • Cottage Cheese – Provides extra protein, and flavor. You can use any fat % you like, but try to find small curd.
  • Salt + Pepper – a must for any egg dish!
basic ingredients for breakfast egg cups, eggs, milk, cottage cheese, salt and pepper

Ingredient Variations for Breakfast Egg Cups

This recipe is the best because you can use your favorite add-ins! Here are some yummy combinations you might want try.

Garden Veggie Egg Cups

  • Egg Cup Base
  • Spinach
  • Tomatoes
  • Mushrooms
  • Cheddar Cheese
ingredients for garden veggie breakfast egg cups spinach, tomato, mushroom, cheddar cheese

French Egg Cups

  • Egg Cup Base
  • Green Onion
  • Smoked Gouda Cheese
  • Asparagus
ingredients for french breakfast egg cups, green onion, asparagus, gouda cheese

Meat Lovers Egg Cups

  • Egg Cups Base
  • Diced Ham
  • Crumbled Bacon
  • Crumbled Sausage
ingredients for meat lovers breakfast egg cups, diced ham, crumbled bacon, crumbled sausage

Greek Egg Cups

  • Egg Cups Base
  • Feta Cheese
  • Tomatoes
  • Kalamata Olives
ingredients for Greek breakfast egg cups with feta cheese, kalamata olives and tomatoes

Spanish Egg Cups

  • Egg Cups Base
  • Black Beans
  • Green Bell Peppers
  • Tomatoes
  • Salsa
ingredients for spanish egg cups with salsa, tomato, black beans, green bell peppers

How to Bake Eggs in Muffin Cups

These egg cups take just a few minutes to whip up!

  1. Preheat oven to 375 degrees F. Spray a muffin tin with non-stick spray.
  2. Whisk together eggs in a large bowl. Add cottage cheese, milk, salt and pepper.
  3. Stir in add-ins for whatever type of egg muffin cup you are making.
  4. Pour egg mixture into muffin tin, filling each cup 3/4 of the way full.
  5. Bake for about 25 minutes, until the centers are completely set. The edges will slightly brown.
  6. Allow to cool for a few minutes before removing and serving.
breakfast egg cups uncooked in a muffin tin and then cooked in a muffin tin

Tips for Making the Best Egg Muffins

  • Make sure you whisk the egg base well so that the whites and yolks of the eggs are thoroughly combined. This prevents clumps of egg white getting cooked and not mixing in.
  • Chop and dice the add-ins very small. You want to get an even mix of add-ins with every bite, and chopping things small is the best way.
  • Spray each muffin cup really well with a good non-stick cooking spray. Eggs are notorious for sticking to things, but if you coat the tin well, they shouldn’t stick.
stack of 3 breakfast egg muffin cups

How Do You Store Egg Muffin Cups?

You can store these in the fridge for up to 5 days or in the freezer for 2 months.

To Store: After they are baked, let them cool and then put in an airtight container. You can reheat in the microwave for 30 seconds from the fridge, and 60 seconds from the freezer. I recommend wrapping in a paper towel from the freezer before microwaving to remove extra water and give a better texture when reheated.

breakfast egg cups variations

Can You Eat Eggs Every Day?

Eggs have gotten a bad reputation over the years because they contain cholesterol.  A large egg contains about 185 mg of cholesterol, and the recommendation from the American Heart Association (AHA) is a limit of 300 mg per day.

So, should you limit your egg intake?  The answer is essentially no.  The recommendation from the AHA can be confusing, and here is why.  It assumes that when you eat more cholesterol from food,  your blood cholesterol increases. But, your body actually doesn’t work that way. The research consistently and reliably shows that the cholesterol you eat has very little impact on how much cholesterol is in your blood.

Your body actually makes its own cholesterol. Lots of it, in fact. Every single day you produce between 1 and 2 grams of it on your own. (That’s 5-10 times the cholesterol in a large egg.) When you eat more cholesterol from foods like eggs, your body produces less of it. And when you eat less cholesterol, your body produces more.  Cholesterol is actually really important in your body. It is in every outer layer of all your cells.  It’s a requirement for growth (in infants and adults). And it’s required for the production of many hormones.

The egg paranoia has been based on the old assumption that eating the yolks will raise blood cholesterol (and increase your risk for artery and heart disease).  And even though the research has disproven the hypothesis — for most of the population — the medical community has been slow to reverse recommendations.  Unless you have medical conditions where your doctor has advised decreasing your cholesterol intake, then eating eggs everyday is just great!

closeup of breakfast egg muffin cups on a white plate

More Favorite Breakfast Recipes

Egg Muffin Cups 24


  • 10 large eggs
  • 1/2 cup cottage cheese
  • 1/4 cup milk
  • 1/2 teaspoon salt or to taste
  • 1/4 teaspoon black pepper

Garden Veggie

  • 1/2 cup spinach diced
  • 1/2 cup tomatoes diced
  • 1/2 cup mushrooms diced
  • 1/2 cup cheddar cheese

Meat Lovers

  • 1/2 cup ham diced
  • 1/2 cup bacon cooked and crumbled
  • 1/2 cup sausage cooked and crumbled


  • 2 tablespoons green onion
  • 1/2 cup smoked gouda cheese
  • 1/2 cup asparagus diced


  • 1/2 cup feta cheese
  • 1/2 cup tomatoes diced
  • 1/4 cup kalamata olives diced


  • 1/2 cup black beans
  • 1/4 cup green bell peppers diced
  • 1/4 cup tomatoes diced
  • 1/2 cup salsa for topping
  • Preheat oven to 350* F. Spray a muffin tin with non-stick spray.

  • Whisk together eggs in a large bowl. Add cottage cheese, milk, salt and pepper.

  • Stir in add-ins for whatever type of egg muffin cup you are making.

  • Pour egg mixture into muffin tin, filling each cup 3/4 of the way full.

  • Bake for about 25 minutes, until the centers are completely set. The edges will slightly brown.

  • Allow to cool for a few minutes before removing and serving. Cool to room temperature before storing.

Serving: 1muffin cup | Calories: 70kcal | Carbohydrates: 1g | Protein: 6g | Fat: 4g | Saturated Fat: 1g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 2g | Trans Fat: 1g | Cholesterol: 157mg | Sodium: 186mg | Potassium: 75mg | Fiber: 1g | Sugar: 1g | Vitamin A: 247IU | Calcium: 37mg | Iron: 1mg

natalie with kids

Natalie Monson

I’m a registered dietitian, mom of 4, avid lover of food and strong promoter of healthy habits. Here you will find lots of delicious recipes full of fruits and veggies, tips for getting your kids to eat better and become intuitive eaters and lots of resources for feeding your family.

Learn More about Natalie

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