This post may contain affiliate links. Please read my disclosure policy.

These healthy baked egg cups make the perfect breakfast meal prep for when you are rushing out the door but still want your protein-packed nutrient dense meal. They also make a great snack as well! And they’re paleo and whole30 friendly!

breakfast baked egg cups in meal prep containerBreakfast Egg Cups Recipe

This recipe goes out to all of those people who LOVE and NEED a good breakfast but don’t always (read: ever) have time in the morning to whip up a freshly cooked eggs! These easy oven baked breakfast egg cups are nutrient dense and so delicious! Make these on Sunday and you’ll be thanking yourself all week you did!

This breakfast meal prep eggs have a sweet potato bottom crust and and you can top with two different options: sunny side up with bacon or veggie omelets! You choose! And if you are feeling it, you can mix and match and make both!

sunny side up baked egg cup

Make it how you like it!

The best part about these baked eggs is that you can truly customize it the way you like it! We love the sunny side up with some crumbled bacon, but you can omit the bacon to make them vegetarian or add in another type of meat like ham!

The veggie omelets have a standard pepper, onion and tomato mix but you can literally add in any veggie here, so long as you chop them up small enough, or precook them.

Here are some other suggestions you can add to the egg muffin cups:

  • zucchini
  • mushrooms
  • spinach
  • cheese
  • ham
  • prosciutto
  • kale

Can you freeze them?

Yes! Make sure to cool the egg cups completely before placing in a air tight container and freezing for up to 1 month. Defrost overnight in the refrigerator and warm it up in the toaster or microwave before serving.

sweet potato crust in muffin tin

Looking for other paleo breakfast recipes?

make ahead baked egg cups on a plate

If you like this meal prep recipe, check out these others:

Pin this recipe to save it for later!

Pin it!

Breakfast Prep Baked Egg Cups

5 from 3 votes
These healthy baked egg cups make the perfect breakfast meal prep for when you are rushing out the door but still want your protein-packed nutrient dense meal. They also make a great snack as well! And they're paleo and whole30 friendly!
Servings 12
Prep Time 10 minutes
Cook Time 20 minutes
Total Time 30 minutes


For Sweet Potato Crust:

  • 1 medium sweet potato
  • 1 tablespoon olive oil
  • 1/2 teaspoon salt
  • 1/2 teaspoon ground black pepper
  • Option 1: Sunny Side Up with Bacon
  • 12 eggs
  • 5 pieces bacon cooked and crumbled
  • salt and pepper
  • Option 2: Veggie Omelet
  • 10 eggs
  • 1/2 cup diced red pepper
  • 1/2 cup diced onion
  • 1/2 cup diced tomato
  • 1 teaspoon salt
  • 1/2 teaspoon black pepper
  • 1/4 teaspoon garlic powder


  • Preheat oven to 350ºF and grease muffin tins very well.
  • Grate sweet potato using cheese grater or food processor.
  • In a bowl mix together sweet potato, oil, salt and pepper. Line the bottom of your muffin tins with the sweet potato mixture. Bake for 20 minutes then remove muffin tins.
  • For Sunny Side up: Crack egg into the muffin tins, sprinkle with bacon and a pinch of salt and pepper.
  • For Veggie Omelet: Scramble eggs in a bowl together with veggies, salt, pepper and garlic powder, and add to divide into muffin tins.
  • Bake for 20-22 minutes or until eggs are set.
  • Remove and serve hot or let cool completely before  store in air-tight container in refrigerator for 3-4 days, or the freezer for up to 1 month.


Calories: 124kcalCarbohydrates: 3.9gProtein: 9gFat: 8.1gSaturated Fat: 2.5gCholesterol: 172mgSodium: 260mgFiber: 0.8gSugar: 1.2g
Course: Breakfast, meal prep
Cuisine: Dairy-free, Gluten-free, Paleo
Author: Lexi

You May Also Like

Secrets to Quick Dinners
Get my practical tips & advice for a healthier life dropped right into your inbox!
newsletter collage

Leave a Comment

Your email address will not be published. Required fields are marked *

Recipe Rating


  1. yes. I want to have these for my weekly meal prep but I like a runny egg. I’m guessing the yolks won’t stay runny once stored in the fridge?

  2. I don’t know how I missed these but wow, they look incredible. If I do sunnyside up, can they be meal prepped in advance?

  3. Can you modify this recipe using a combination of eggs and egg whites to lower the fat content?

  4. I really like this idea. Can you tell me which part you pre-prepare? The potato nest or the whole beautiful thing.
    Thx for sharing!

  5. How long do these stay good in the fridge for? I’m trying to figure out how to make some breakfast meal preps!

  6. “Make sure to pray/grease your muffin tins so the sweet potato nests do not stick” … I always pray they don’t stick 🙂

  7. Why is no one mentioning the brilliance of BUILT-IN BACON!? This looks like the best possible version of one of those breakfast sandwiches at Starbucks (which are amazing, by the way).

  8. I make egg cups at the beginning of every week for quick, grab and go breakfast. But, I love the idea of adding sweet potato as the crust. Can’t wait to try these out.

  9. Those eggs are cooked to UTTER PERFECTION! Not too runny but not too hard either. Oh wow, I am completely craving eggs! 😉

  10. These are just darling, and I love how much quality protein they pack for busy on-the-go days! And I toootally agree – lovin’ eggs any time of the day! 😀