These Healthy Baked Egg Cups are simple and so easy to modify depending upon what you have in your fridge! Perfect for meal prep too!

Healthy Baked Egg Cups are an easy breakfast option that is meal-prep friendly! (Dairy-Free + Whole30 + Paleo)

Healthy Baked Egg Cups

We love this recipe for weekly meal- prep or just a fun weekend breakfast option! The recipe is so easy and the ingredients are so simple! Plus, you can easily change up the ingredients depending upon what you have in the fridge. Love serving with some American Fries if we are serving these for brunch!

Why You Will Love This Recipe

  • Size:  I love frittata, but sometimes its nice to have some smaller portions like this! My kids love them!
  • Customizable: Of course you can follow the directions below, but feel free to mix things up a little depending upon what you have in your fridge!
  • Meal-Prep: I love making these on Sunday and eating them for breakfast throughout the week!

Can You Freeze Them

Yes! Just cook them as directed. Let them cool completely and then place them on a cookie sheet and place in the freezer for at least 1 hour. The place them in a storage bag (a silicon Stasher Bag would work great) and store in the freezer for up to 3 months.

How to Reheat Frozen Egg Cups

To use from frozen simply take one or more out of the freezer and let thaw in the fridge overnight. In the morning you can eat it cold or reheat in the microwave (I recommend gently wrapping them in a damp paper towel), toaster oven or regular oven!

Recipe Variations

You can make this recipe what you want (or based on what you have in your fridge). The cooking time should really stay the same. Here are a few suggestions:

  1. bacon
  2. kale
  3. tomatoes
  4. potatoes (although you would need to cut them very small or they wouldn’t cook enough in the oven)
  5. zucchini
  6. beef
  7. mushrooms
  8. jalapeños
  9. onion

Made this recipe and loved it?! We would love it if you would take a minute and leave a star rating and review – it is also helpful if you made any substitutions or changes to the recipe to share that as well. THANK YOU!


Healthy Baked Egg Cups – perfect for meal-prep and so easy to make! Dairy-free + Whole30 + Paleo!


  • 5 eggs
  • 1/4 cup unsweetened almond milk
  • 1/2 teaspoon salt
  • 1/4 teaspoon ground black pepper
  • 1/23/4 cup ground pork sausage (see notes)
  • 1/23/4 cup fresh spinach, ripped into small pieces
  • Approximately 1/4 of a large red bell pepper, diced


  1. Preheat oven to 350 degrees F.
  2. Spray muffin tin with olive oil and set aside.
  3. In medium bowl whisk together eggs, unsweetened almond milk, salt and pepper.
  4. Cook pork sausage over medium heat.
  5. Take muffin tin and add a tablespoon or so of cooked pork. a tablespoon of ripped spinach and a tablespoon of diced bell pepper to each muffin tin.
  6. Pour the egg mixture over top, filing so there is a little room at the top (it will expand and rise as it is cooking – but then will deflate once it cools).
  7. Place in the oven and cook for 17 minutes.
  8. Remove from oven, if the very top isn’t fully cooked, return to oven for 2-3 minute increments until fully cooked.


  • Pork Sausage: I use seasoned (Whole30 compliant) pork sausage for this recipe.  If you can only find simple ground pork, season it as it is cooking with a pinch salt, pepper and a little bit of fennel.
  • Bell Pepper: Feel free to use a different color of bell pepper – whatever you happen to have in your fridge will work.
  • Variations: you can really use the base of this recipe and modify in a variety of different ways! You can substitute cooked bacon for the sausage, kale of the spinach and mushrooms for the bell peppers!
  • Egg Cups: Feel free to use silicone muffin tin liners if you want. It shouldn’t change the cook time, but again if the tops aren’t quite cooked after the stated cook time, continue cooking in 2-3 minute increments.  The eggs will continue to cook a bit after they come out of the oven.
  • Storage: store in an airtight container in the refrigerator for up to 4 days.