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!

WHAT YOU WILL NEED
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.
HOW TO MAKE EGG AND CHEESE TORTILLA CUPS
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!

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!


Mini Egg and Cheese Tortilla Cups
Ingredients
- 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
Instructions
- 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!
Video
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.

4” rounds fit better. I added red bell pepper and green onions then topped with chopped fried bacon pieces. Yum!
Delicious. I used 3 eggs, have to watch my carbs, diabetes demands it.
I am going figure out the nutritional values.
I used small corn tortillas, perfect size for my muffin pan
Thanks for this wonderful recipe.
looks very promising, however I would like to not waste any food. So do you have a very good suggestion to use the leftover tortillas pieces,,,,,,,,,,,,,,,,,,,,,being food frugal and re purposing is important to me. Always looking for new ways to stretch a dollar or food. Penny saved and all 🙂
U could fry them and top with cinnamon sugar for snacking or ice cream/yogurt topping
Make chips or crispy pieces from the scraps
For the left over tortillas, I’m going dip them in cinnamon sugar and deep fry them for a bit. A little sweet dessert with vanilla ice cream!
These are fantastic. I made these for my 5 kids aged 9-1 and they loved them. I only used 5 eggs opposed to 8 because that is all our chickens supplied us that morning, but I followed the rest of the recipe. They baked well and we’re light and airy. These will definitely be a regular in our house. I can’t wait to add pepper jack cheese and jalapeños to some, mushrooms and different types of cheeses, as well as sausage or bacon for the meat eaters in my family. The sky is the limit with these. Thank you for this recipe.
So happy the little ones enjoyed them!
Recipe says sour cream instructions say cream cheese what is correct
It’s sour-cream 🙂
These were just delicious!! I used low carb tortillas. These will be made often in my house!
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!
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.
could you make these ahead and reheat?
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
I bet you could use those little taco boat shells for this
Can you put a little ham pieces in them
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!
That’s genius!
How do you reheat them?
Are these intended for actual mini muffin pans or regular muffin pans?
They are the standard size muffin pans.