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:
- bacon
- kale
- tomatoes
- potatoes (although you would need to cut them very small or they wouldn’t cook enough in the oven)
- zucchini
- beef
- mushrooms
- jalapeños
- onion







Other recipes you might like:
- Ultimate Healthy Breakfast Casserole
- Make Ahead Breakfast Stuffed Sweet Potatoes
- Breakfast Salad + Bacon Vinaigrette
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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!
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Baked Egg Cups
- Prep Time: 15 minutes
- Cook Time: 17 minutes
- Total Time: 32 minutes
- Yield: 6 egg cups 1x
- Category: Breakfast
- Method: Oven
- Cuisine: American
Description
Healthy Baked Egg Cups – perfect for meal-prep and so easy to make! Dairy-free + Whole30 + Paleo!
Ingredients
- 5 eggs
- 1/4 cup unsweetened almond milk
- 1/2 teaspoon salt
- 1/4 teaspoon ground black pepper
- 1/2 – 3/4 cup ground pork sausage (see notes)
- 1/2 – 3/4 cup fresh spinach, ripped into small pieces
- Approximately 1/4 of a large red bell pepper, diced
Instructions
- Preheat oven to 350 degrees F.
- Spray muffin tin with olive oil and set aside.
- In medium bowl whisk together eggs, unsweetened almond milk, salt and pepper.
- Cook pork sausage over medium heat.
- 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.
- 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).
- Place in the oven and cook for 17 minutes.
- Remove from oven, if the very top isn’t fully cooked, return to oven for 2-3 minute increments until fully cooked.
Notes
- 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.
Nutrition
- Serving Size: 1 egg cup
- Calories: 95
- Sugar: 0.2 g
- Sodium: 331.6 mg
- Fat: 7 g
- Carbohydrates: 0.6 g
- Protein: 6.7 g
- Cholesterol: 162.2 mg
Keywords: baked egg cups, egg muffin cups, egg cups recipe


Carol says
Made mine with just egg, bell pepper and spinach. Very good and easy. They puffed up while baking and then deflated while cooling. Is that normal or did I cook too long? They taste great though.
Erin says
Hi Carol – some puffiness while cooking is totally normal and then it should reduce after cooling!
Carli says
These are perfect! Easy to make, last all week and are delicious. Big fan!
★★★★★
Erin says
Thank you, Carli! Thank you for coming back to leave a review!
Julie says
Id I want to bake this in a pan, what size would I use?
Erin says
Hi Julie – I have only ever made these in muffin tins!
Janna says
Thanks for the recipe. Very tasty! Any idea how many calories?
Jale says
How long can you store in the fridge? Everyone loves these. Also perfect colors for Christmas!
★★★★★
Erin says
Hi Jale! So glad everyone is enjoying them! They last about 3-4 days in the refrigerator (in an airtight container).
Nicole says
Hi! I am excited to try these this week. How long would they last in the fridge? Thank you!
Erin says
Hi Nicole! They should last about 4-5 days!
Molly says
If you’re looking for something easy, healthy and yummy this is it! I am a busy Mom of 3 & school mornings are hard. Finding something health & easy is tough.
These are so good! I made a double batch, freeze them and the night before I pull one out & stick it in the fridge to thaw, in the morning I wrap it in a moist paper towel, heat it up in the microwave and breakfast is served.
★★★★★
Erin says
Thanks, Molly!!! I so appreciate you taking the time to leave your feedback – glad you are enjoying them!
Courtney says
I made a double at batch of these for breakfast this week they turned out great! They stay moist even after reheating and they have great flavor. I’ll definitely make these again.
★★★★★
Katie says
Do you think these could be frozen?
★★★★★
Violet says
Love this recipe! Can I freeze these and if so, how should I reheat them if I freeze them?
Patty says
Tried these but they were a super weird texture in the middle. Sm I missing something?
Erin says
Hi Patty – did you let them cool all the way?
Jessica says
I love a good egg bake, and this one was fantastic! It is really going to help me prep my mornings and stay within my W30 food freedom. My kids and I made these this morning and we will be keeping them on the menu when school starts back up. So yummy!
★★★★★
Nicole says
This recipe is great! I doubled it to make 12 egg cups. They were easy to make in my silicone pan too!
★★★★★
Erin says
So happy to hear that, Nicole! Thank you so much for taking the time to leave your review + feedback – I really appreciate it!
Sarah Thompson says
The egg cups turned out amazing! I did turkey sausage, an orange pepper, spinach, some garlic, and I sauteed onions on the side. My family loved it!
★★★★★
Erin says
So happy to hear that, Sarah! Thank you so much for taking the time to leave your review + feedback – I really appreciate it!
Rebekah says
This was SO easy and yummy!! I made extra to save for breakfast this week 🙂
★★★★★
Erin says
So happy to hear that, Rebekah! And thank you so much for coming back to leave a review + feedback – I really appreciate it!
Kaitlyn says
Can these be frozen or will it ruin the texture? I’ve ever tried freezing eggs before but I was thinking about making a double batch and freezing some to have them ready to go for breakfasts.
cathy says
Can this be doubled and used with a 12 opening muffin tin?
Erin says
Yes! It definitely can be doubled!
Suzanne Holt says
I made this for my gluten-free husband and he loved them!
Erin says
So happy to hear that, Suzanne! Thank you for taking the time to leave your feedback!
Nancy says
Perfect little. breakfast!
★★★★★
Erin says
Yay! So happy to hear you enjoyed it, Nancy! Thanks for taking the time to leave your feedback – I really appreciate it!
Tina says
Question: Do you know what a ‘serving’ is for Whole30 compliant breakfast? Is it one person per muffin? Thank you.
Erin says
Hi Tina! Here is a link to the Whole30 Meal Template: https://whole30.com/downloads/whole30-meal-planning.pdf – based off of that I would say 1-2 of these muffins would be perfect (I would personally do 2 to make sure I was full) – but everybody is different! Hope that helps!