Egg, veggie, and cheese omelets baked in tortilla cups for a super convenient and fun way to have breakfast! These mini egg and cheese tortilla cups make a great make-ahead breakfast and can be frozen too.

Sunday morning brunch is one of my favorite meals of the week. I look forward to it all week and because it’s the only time we get to have breakfast together as a family, without rushing out the door that is.

Problem is that my daughter is very picky so I’m always trying to develop recipes that she can enjoy along with us. At first, I was hesitant to add peppers to the dish but I had to because they are so good in eggs. She loved these mini egg and cheese tortilla cups and so did we!

This is as easy as it can get folks. These mini egg and cheese breakfast bites are perfect for kids and adults. They are also great on the go, take them to school or work, and watch the compliments roll in!


The mixture I used to fill the tortillas is very basic yet absolutely delicious. You’re going to need some flour tortillas, any type of shredded cheese you like ( I used a mixture of cheddar and mozzarella), sour cream (you can also use heavy cream or milk), and veggies. I used a mixture of colored bell peppers and onions.


It all starts with cutting your small flour tortillas into even smaller circles. You want the circles to fit into a muffin tin without any excess tortilla popping out.

Next, simply whip the eggs and sour cream, season with salt and pepper, and pour into the prepared tortilla cups. Sprinkle with your favorite mixture of veggies and sprinkle with cheese and all that’s left to do is bake!

Easy Mini Egg and Cheese Tortilla Cups

You want to bake them until the tortilla crust is super crispy and the eggs are cooked through. If you like extra cheese, feel free to sprinkle more cheese onto them halfway through cooking.

Wanna spice it up? add some blanched broccoli, diced bacon, potato hash, or any else you would usually use in an omelet!

I advise you to make extra because these little bites will not last! my daughter literally finished half of them before they even hit the table!

4.72 from 28 votes

Mini Egg and Cheese Tortilla Cups

By: Layla
Egg, veggie, and cheese omelets baked in tortilla cups for a super convenient and fun way to have breakfast! These mini egg and cheese tortilla cups make a great make-up breakfast and can be frozen too.
Prep5 minutes
Cook15 minutes
Total20 minutes
Servings 12 tortilla cups


  • 8 eggs
  • 1/2 cup sour cream, or milk, or heavy cream
  • 1 cup shredded cheese, you can use any type, I used cheddar and mozzarella
  • diced veggies, I used a mixture of bell peppers and onions
  • 2 extra large tortilla or 8-12 small
  • salt and pepper to taste


  • Heat oven to 350 degrees F. Grease a 12 cup muffin pan and set aside.
  • Stack tortillas and cut out 12 small (about 3.5 inch) round circles out of the tortillas, you can use anything that has a rim, can, cup, bowl. If you are using big tortillas cut the four circles out of one tortilla. If you are using small tortillas you will only be able to cut one out of each tortillas. Press each wrap circle into 12 greased muffin tins using your fingers. It's okay if it doesn't fit perfectly, it will balance out after you add the eggs. Set aside.
  • In a medium bowl, whip the eggs and sour cream until fully combined, it's okay if it's a little lumpy, the sour cream will bake into the eggs. Add half of the cheese and set half aside, sprinkle salt and pepper to taste. Pour the equally into the prepared muffin tins ( into the tortillas), then sprinkle the veggies as desired.
  • Bake for 10 minutes, after 10 minutes sprinkle the rest of the cheese on the eggs, continue baking for 3-5 minutes more or until cheese is bubbly and tortilla crust is golden. Serve warm, eat using a fork or grab one and bite right in!



Serving: 1tortilla cup, Calories: 107kcal, Carbohydrates: 4g, Protein: 6g, Fat: 7g, Saturated Fat: 3g, Cholesterol: 121mg, Sodium: 143mg, Potassium: 95mg, Fiber: 1g, Sugar: 1g, Vitamin A: 670IU, Vitamin C: 16mg, Calcium: 80mg, Iron: 1mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Additional Info

Course: Breakfast
Cuisine: American
Keyword: cheese, egg, tortilla
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  1. made these today added a bit of chorizo to spice it up And they are sublime! A perfect packaBle breakfast to reheat at work on the days i go to the gym. ThAnks for Sharing!

  2. 3.5 inch ciRcles only go halfway up the muffin tin cups. 4” circles would be much better. As such i had lots of egg mixture left and had to cut more circles to use the egg. They were not neArly set After 10 mins so i let them cook at least 10 more before putting the cheese on top. This concept is greAt but the author doesn’t seem to have actually done it orvthe directions would be more accurate.

  3. Will use tortilla cup idea with spaghetti squash bake; Needed recipe which i can make ahead and just reheat last minute before guests arrive.
    Thank you

  4. I bet you could use those little taco boat shells for this

  5. Great recipe! I saw these mini tortillas at the grocery store recently so you don’t have to cut them out! I am making these in bulk to store in the freezer to grab & go on my way to work. Thanks!

      1. You can microwave but I find re-heating in the airfryer works best!

  6. Are these intended for actual mini muffin pans or regular muffin pans?

  7. This recipe was really good. I tried both flour and corn tortillas and preferred the flour because they let the egg flavor shine through and the corn tortillas taste and texture was too strong. I had to cook them about 10 minutes longer than the recipe recommended. I used green onions. My husband thought mushrooms would be a good addition. I’ll try adding crumbled bacon next time. This would be a fun recipe to use when RV camping with friends because they’re cute and can be eaten without utensils. I reheated two the next morning for one minute on high in the micro wave and they were even better with stronger flavor the next day.

  8. Absolutely delighted! Used corn tortillas. I love the comment about toasting the extra strips for dipping! Genius!

  9. Awesome recipe! I opted to use almond milk instead of the sour cream. Still came out light and fluffy. Spread a little bit of mashed avocado on top before serving, perfect! 🙂

  10. These egg, cheese and veggie cups were awesome tasting! I’m always looking for new recipes to cook for my husband and I that are healthy, easy, and convenient – this recipe fits all 3. I use low carb wheat tortillas, and I put in red peppers and jalapeño peppers for added kick along with the chopped onion. I double the recipe and save the rest of them in the fridge so all I have to do is pop them in the microwave in the morning for breakfast. =) GREAT RECIPE!

  11. Sounds good and you can alter the veggies, you can also cut the left over tortilla into strips and toast them to eat with the eggs.

  12. Looks great!! Don’t have tortillas, can I sub for naan?

    1. I’ve never tried naan before. I would imagine it’s too thick. If you do give it a try, please let us know!

  13. I find these very interesting, and if you make a little more twist these kind of food will definitely abig hit for kids snack.

  14. These look so delicious and easy to prepare as well, that’s always a good thing. I am pinning this recipe, so I can give it a try soon! Thanks for the recipe!

  15. These look awesome! I actually used your recipe but modified it a little bit. I had left over shredded chicken and added it to the mix! They came out sooooo goood!!

  16. Just tried these & they were great! Took me a few minutes longer in the oven & I used corn tortillas : )

  17. Found this on Pinterest– I’m curious if they can be made ahead and reheated? Looks delicious and I’d love to make these the night before and reheat and eat the next morning. Thanks for your time!

  18. Can Greek yogurt be used in place of sour cream? Or does that not bake as well?

    1. Due to allergies in my family we replace any recipe that calls for sour cream with yogurt and have never had a taste or cooking issue. I would assume greek yogurt would work just as well.

      1. Yes, I usually replace sour-cream with yogurt in recipes and it works just as well, although I would suggest using greek yogurt because it’s a little more richer. Best of luck!

        1. this may sound odd but in lieu of a few items if you split the difference using half mayonnaise and half sour cream and then add green chilies finely diced, anywho I suppose it’s like a breakfast meatloaf haha meaning the ingredients are truly limitless but the mayo really creates a nice soft texture and works very well as a binder! anyway this is just such a great idea thank you so much can’t wait to make a bunch of them this weekend

  19. Began meal planning and came across this. I too am a picky eater like your daughter but this has me intrigued. Thanks for the recipe. Excited to try it!

  20. I just made these, sooo good. I had a lot of egg mixture leftover. I sprayed mini loaf pans and made mini loaf omelettes. I added fresh herbs to the mini loaves. Very delicious. I had to bake these longer than cooking time though. Delicious no matter what, a great recipe. Portable too! I added a side of salsa to dip. Thanks for sharing.

  21. Egg and cheese in tortilla cups. Who would have thought? These are absolutely delicious!

  22. Love this! So cute and I bet they freeze well so you can bake a bunch in advance!

    1. yea freezing them is a great idea! Thanks, Leah! 🙂

      1. Do you freeze after cooking? How long can you store? What are reheating instructions?

        1. Feel free to freeze them as soon as they cool and for reheating, you can reheat in the microwave for 2 minutes or in the oven at 375 until warmed through.

  23. What a seriously fun way to have breakfast!

    1. Thanks so much for all your sweet comments, jackie! Have a great week 🙂