Breakfast Prep Baked Egg Cups

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:

On-The-Go Baked Egg Nests
Yields 12
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Prep Time
10 min
Cook Time
45 min
Total Time
55 min
Prep Time
10 min
Cook Time
45 min
Total Time
55 min
Two Ways
  1. Over easy or omelette style
For both
  1. 12 organic or farm-fresh eggs
  2. 1 medium sweet potato
  3. 1 tsp extra-virgin olive oil
  4. Himalayan sea salt and freshly ground pepper, to taste
  5. Optional: 5 slices nitrate-free bacon, cooked
For Option 2- Omelettes
  1. Veggies of choice: tomato, onion, spinach, broccoli, mushrooms
  2. Himalayan sea salt, to taste
  3. Freshly ground pepper, to taste
  4. 1/4 tsp garlic powder
  5. 1/4 tsp onion powder
  1. 1. Preheat oven to 350 and grease muffin tins
  2. 2. Grate sweet potato using cheese grater or food processor, squeeze out excess water
  3. 3. Mix 1 tsp oil, salt, and pepper with sweet potato
  4. 4. Line the bottom of your muffin tins with the sweet potato mixture
  5. 5. Let bake for 20 minutes then remove muffin tins
  6. 6.
  7. Option 1: Over easy: crack egg into the muffin tins (add optional pre-cooked bacon)
  8. Option 2: Omelettes: mix eggs in a bowl, add in veggies, garlic powder, onion powder, salt and pepper, add into muffin tins
  9. 7. Bake for 20-25 minutes or until eggs are firm
  10. 8. Remove and serve hot
  11. 9. Store in air-tight tupperware in refrigerator
  1. Make sure to spray/grease your muffin tins so the sweet potato nests do not stick
Lexi's Clean Kitchen