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Healthy Breakfast Egg Muffin Cups

DIY healthy breakfast egg muffin cups using whatever veggies you have in your fridge. These low carb, easy egg muffins are simple to make and perfect for reheating throughout the week! A delicious, protein-packed breakfast recipe that’s gluten free, paleo, vegetarian and keto-friendly.

Prep Time
10 mins
Cook Time
25 mins
Total Time
35 mins

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Welcome to my most basic, yet most addicting and simple breakfast recipe: Healthy breakfast egg muffins. 😍

I wanted to share a recipe with you to only inspire you to eat healthier in the new year, but to also help you easily meal prep for breakfast. Also, I realized that many of my breakfast recipes are on the sweeter side, so this one is for all my savory lovers.

Look I get it, many of you are busy little bees. You work hard, you want to cook healthy and you want to nourish your body at the same time. But it’s difficult to plan ahead and the last thing you want to think about on a Sunday is cooking for the rest of the week.

The easiest solution is to pick recipes you are actually excited about!

veggies in a muffin tin to make breakfast egg muffin cups

Ingredients in these easy egg muffins

I don’t know about you, but I love when I can make recipes out of what I already have in my fridge. Case in point: these breakfast egg muffins in portable cup form. To make them you’ll need:

  • A dozen eggs
  • Almond milk (or milk of your choice)
  • A mix of your favorite veggies! I used spinach, tomatoes (I used roma tomatoes), mushrooms and jalapeño
  • Salt & pepper
  • A sprinkle of cheese if you want!

I love that these healthy egg muffin cups are cheap, easy and customizable. I used a carton of eggs, leftover veggies I had from the previous week, a splash of milk and that’s basically it. Bake them up and you have breakfast (or snacks) ready for the week ahead.

breakfast egg muffin cups in a muffin tin

How long will healthy breakfast egg cups keep in the fridge?

These healthy egg muffin cups will keep in the fridge for up to one week, so you can enjoy a healthy, easy on-the-go breakfast all week long. Simply place your completely-cooled egg muffin cups into an airtight container and pop them in the fridge.

When you’re ready to eat them, just reheat the ones you want to eat in the microwave for 30-60 seconds. You can also reheat them in the oven at 350 degrees F for about 5-10 minutes.

Freeze and reheat them for later!

  1. To freeze egg muffin cups: let the breakfast egg muffins completely cool, then transfer them to a freezer-safe container. You can freeze them up to 3 months.
  2. To reheat frozen egg muffin cups: you can either let them thaw in the refrigerator before reheating them in the microwave, or you can simply place them straight into the microwave and heat them for about 1 minute.

egg muffin cups in a container with avocado and salsa

Customize these breakfast egg muffin cups

You can easily make these low carb egg muffins your own! Here are a few suggestions for mix-ins:

  • Broccoli cheddar: add 1 cup finely chopped broccoli + 1/2 cup of shredded cheddar cheese
  • Caprese: 1 large roma tomato, 2 cups spinach + 1/2 cup shredded mozzarella cheese
  • Bacon + cheddar: 1 package of cooked bacon, chopped (regular or turkey bacon) + 1/2 cup shredded cheddar cheese
  • “The Denver”: 1 diced green bell pepper, 1 small yellow onion and 1/2 cup diced ham (optional: add mushrooms!)
  • Southwestern: 1 diced green bell pepper, 1 diced red bell pepper, 1 diced jalapeño, 1/2 cup shredded Mexican cheese (top with avocado, cilantro & hot sauce!)
  • Spinach + feta: 2 cups spinach, 1 roma tomato + 1/2 cup feta crumbles

What to serve with egg muffin cups

The options are endless for what to serve with these easy, healthy egg muffins. Here are some great additions to your plate:

The options are endless! These easy egg muffin cups are perfect for bringing to a brunch and enjoying as a side.

More savory breakfast recipes to try:

Savory Chicken Sausage, Egg and Cheese Muffins (keto + low carb)

Jalapeño, Pepper Jack & Turkey Bacon Quiche with Potato Crust

Veggie Packed Freezer-Friendly Breakfast Burritos

Spinach & Goat Cheese Quiche with Sweet Potato Crust

Sweet Corn Honey Jalapeño Zucchini Cornbread Waffles with Turkey Bacon & Eggs

You are going to love how simple and nourishing these are. If you make them, be sure to leave a comment below and rate the recipe. You can also tag me on Instagram #ambitiouskitchen!

Healthy Breakfast Egg Muffin Cups

4.91 from 11 votes
egg muffin cups in a container with avocado and salsa
Course Breakfast, Brunch, Dairy Free, Gluten Free, Grain Free, Low Carb, Meal Prep, Paleo Friendly
Cuisine American
Keyword breakfast egg muffin cups, easy egg muffins, egg muffin cups, healthy breakfast egg cups
Prep Time 10 minutes
Cook Time 25 minutes
Total Time 35 minutes
Serves 6

DIY healthy breakfast egg muffin cups using whatever veggies you have in your fridge. These low carb, easy egg muffins are simple to make and perfect for reheating throughout the week! A delicious, protein-packed breakfast recipe that's gluten free, paleo, vegetarian and keto-friendly


  • 2 cups spinach, chopped
  • 1 large roma tomato, seeds removed and diced
  • ½ cup baby bella mushrooms, diced
  • 1 jalapeño, seeded and diced
  • 12 eggs
  • 1/4 cup unsweetened almond milk (or any milk)
  • ½ teaspoon salt
  • Freshly ground black pepper
  • Optional: 3/4 cup shredded cheddar cheese


  1. Preheat oven to 350 degrees Fahrenheit. Spray a muffin tin with nonstick cooking spray.
  2. Divide spinach, tomatoes, mushrooms, and jalapeño evenly between 12 muffins in the tin.
  3. In a large bowl whisk together eggs, almond milk, salt and pepper until well combined.
  4. Fill each muffin about 3/4 way full with egg mixture, pouring over the veggies already in each tin. If using cheese, add 1 tablespoon on top of each egg muffin.
  5. Bake for 25-30 minutes until eggs are set and puff up in the tin. Let muffins cool for a few minutes, then run a butter knife around the edges of each cup and remove. Serves 6 (2 egg cups each).

Recipe Notes

To meal prep: Make these ahead of time and pack in glass containers with ½ an avocado and ½ a cooked sweet potato for a well balanced breakfast.

Servings: 6 servings (2 egg muffin cups each)
Serving size: 2 egg muffins without cheese
Calories: 131kcal
Fat: 8.4g
Saturated fat: 2g
Carbohydrates: 1.9g
Fiber: 0.6g
Sugar: 1.3g
Protein: 12.7g

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