The Ultimate Guide to Breakfast Egg Cups

Q: How to Reheat Baked Tortilla Egg Cups?

If you need to eat your Baked Tortilla Breakfast Egg Cups first thing in the morning - which is probably what you’re looking for in the first place by making this recipe! You should only require about 30 seconds up to 1 minute to reheat your egg cups in the microwave. Keep a close eye on them to ensure they don’t overheat!

✦ Join the Kitchen

As I describe in my motivational guide to exploring your potential in the kitchen Make Cooking Fun!! free motivational guide, being aware of what’s in your kitchen can inspire your creativity! You’ll see with these egg cups that there are so many options you can use based on what vegetables and/or meat is in your fridge! If you’ve got some vegetables and/or protein to eat, then using them in your egg cups is a fantastic and delicious way to use them!

Six baked tortilla egg cups with eggs and herbs on a white plate.

Some people find that eggs are a pesky protein, but these Tortilla Egg Cups are an easy way to cook them! Eggs no longer have to be a pesky protein by trying out these egg cups as part of your Live to Cook one-month challenge! Get started on your cooking journey for free today by signing up to my email newsletter, plus you’ll get all of my new recipes delivered right to your inbox, including lots of breakfast inspiration!

To see these 6 Baked Tortilla Egg Cup ideas in action to have breakfast ready for you all week long for the busy mornings ahead, be sure to watch the video at the bottom of this post! If you’re not already, please subscribe to my YouTube channel, and don’t forget to press the bell button to be notified when all of my video recipes go live! Let’s get cooking!

Golden baked tortilla egg cups filled with eggs and vegetables on a white plate.

Is there a Difference between Using COrn Tortillas and Flour Tortillas?▼

Yes, there will actually be a considerable difference between which type of tortilla you choose to use in these egg cups. I used corn tortillas, and the first thing that I noticed is that they’re not as pliable as flour tortillas. Therefore, you’ll need to wrap them in a damp kitchen cloth or paper towel so that they soften up. They also are likely to break as you add them to the muffin tray. If this happens, that means the egg mixture will escape the tortillas, so the end product of your egg cup will be a little softer. For a crunchier exterior, then you’ll want the flour tortillas so that they hold their shape and keep all of the egg mixture inside.

From a nutritional standpoint, corn tortillas are gluten-free, so if you have a gluten intolerance, you’ll need to use corn tortillas. I personally prefer the taste of corn tortillas over the taste of flour tortillas, which is why I had them on hand. However, I do want to try this recipe out with flour tortillas to really determine the difference! All that being said, you can use any kind of tortilla you want, just know the differences!

Stack of thin corn tortillas on a white plate with a muffin tin visible in the background

Why You’ll Love This Baked Tortilla Egg Cup Recipe!

Easy to make
Requires little time to make
You only need a muffin tray and a bowl to whisk your eggs!
Vegetarian-friendly
Can be gluten-free
High in protein
Lots of options to customize!

Three golden baked egg cups filled with creamy filling and herbs, served on a white plate.

Tips for Satisfying Baked Egg Cups

If using corn tortillas, wrap them up in a damp paper towel or kitchen towel and then microwave them to warm up to help make them softer and more pliable to fit the muffin tray moulds.
While you can pick whichever order to prepare the fillings for the egg cups, my favourite ones were where I had cheese at the bottom and the top of the egg cups.
Trying shaking things up and using flour tortillas to get a crispier texture as those tortillas are less likely to break and fill form a wonderful crust to hold the eggs.
Instead of whisking the eggs, you can opt to directly break 1 egg into each of the muffin moulds.
A good way to check whether the eggs are set is to shake the baking tray and see if the egg are runny in the center.

Golden-brown baked egg cups in a muffin tin, served on a white plate.

Tools Needed to Make Baked Egg Cups

Five golden baked tortilla breakfast cups with herbs in a muffin pan, served on a white plate.

Ingredients in Tortilla Breakfast Cups

To get all ingredients and their quantities and to save the recipe for later, scroll to the bottom of this post for the FULL PRINTABLE RECIPE or press the “Jump to Recipe” button. You can also use the recipe card to scale the recipe based on how many egg cups you want to make. By default, this recipe yields 12 Tortilla Egg Cups.

Ingredients for breakfast tortilla cups laid out: diced red onion, green pepper, jalapeño, and orange bell pepper in a bowl, with cooked ground meat, crispy tortilla rounds, chopped cilantro, eggs, and oil.

For the Base

Eggs: Large eggs. They’re the main ingredient here! You may need more or less eggs depending on the size and the depth of the holes of your muffin tray.
Mini tortillas: I used corn tortillas, but you can use flour tortillas. I recommend flour tortillas actually so that they keep their shape while baking.
Cheese: I’m using a Mexican blend of cheese from my local grocery store. If you want the cheese “pullyness” plus flavour, I recommend a blend of mozzarella and cheddar. More generally, a blend of a soft cheese and a semi-hard cheese will give you the best results.
Olive oil: Spray a bit of olive oil in your muffin tray so that the egg cups doni’t stick.
Salt & pepper: Essential seasoning in our egg cups.

Buttered egg fried rice in a white bowl with hash browns and a purple cabbage salad visible in the background.

For the Vegetarian Breakfast Egg Cups

Hash browns: You can use frozen hash browns, as I did here to save some time. However, for a really made-from-scratch breakfast, you can make your own hash browns! Alternatively, you could make diner-style hash browns.
Jalapeños: Sliced into circles.
Bell peppers: Red and green are my preference. Finely dice them.
Onions: Any onion will work, but red onions are my favourite. You’ll want to dice them.
Green onions
Chives

Diced red onions, green peppers, and orange bell peppers in a white bowl with crispy hash brown patties and chopped green onions on the side.

For the Meaty Breakfast Egg Cups

Sausage: I’m using a hot Italian sausage from my grocery store, but if you really want this to be a fresh and entirely homemade breakfast, try making your own! I recommend either my Mild Italian Chicken Sausage if you don’t eat pork and want a poultry option. If you do like pork, try out my Spicy Calabrian Chilli Sausage or my Pork and Bacon Sausage.
Bacon: Chopped bacon bits. No need for this if you’re using my Pork and Bacon Sausage!
Hash browns: I’ll be adding hash browns to my egg cup with bacon, but there’s nothing stopping you from also adding it to an egg cup with sausage!
Onion: I’ll add diced onions to the egg cup with bacon.
Green onions: For demonstration, green onions will be added to my egg cups with sausage.

Scrambled eggs with crispy bacon strips in a white bowl, served with crackers and olive oil on the side.

How to Make This Easy Tortilla Breakfast Cups Recipe

Preheat the Oven: Set to 350°F (175°C) and grease a 12-cup muffin tin with cooking spray or oil.

Crack all the eggs in a large bowl or measuring cup and season with salt and pepper.

Cracked eggs in a glass measuring cup with oil, surrounded by ingredients including tortillas and chopped vegetables on a gray countertop.

Cracked eggs whisked in a Le Creuset measuring cup with a red lid, surrounded by prepared ingredients and tortillas on wooden plates.

Prepare the Tortillas: Slightly warm the corn tortillas by wrapping them in a damp kitchen towel and microwaving for 30 seconds to 1 minute.

Stack of warm corn tortillas wrapped in a white kitchen towel, ready to be molded into egg cups.

Warm corn tortilla pressed into a muffin cup to form an egg cup shell

Gently press each tortilla into a muffin cup, folding as needed to fit.

Pick whichever filling options from below and prepare the tortillas:

Flour tortillas pressed into muffin cups with various filling ingredients and condiments arranged nearby.

Hand placing folded tortilla into muffin tin cups lined with partially pressed tortillas for egg cups.

For the Vegetarian Breakfast Egg Cups

Twelve tortilla cups pressed into a muffin tin with various vegetarian fillings like cheese and vegetables visible inside.

Tortilla cups filled with cheese, vegetables, and fresh herbs arranged on a white plate before baking.

Vegetarian Filling Ideas: 1) cheese, chives, jalapeño; 2) cheese, green onions, hashbrown pieces; 3) peppers, onions, jalapeño, cheese; 4) peppers, onions, hashbrowns, cheese, chives

Hands filling crispy wonton cups with vegetables and toppings in a muffin tin for vegetarian egg cup appetizers.

Multiple crispy wonton egg cups filled with diced peppers, onions, and other toppings on a white plate.

For the Meaty Egg Cups

Mini egg cups with various fillings including purple onions, cheese, and cooked ingredients arranged in a muffin tin.

Egg cup muffins in a muffin tin with various vegetarian fillings including cheese, hash browns, and vegetables, some partially filled with egg mixture.

Egg cups in a muffin tin filled with hash browns and cheese, topped with golden-brown baked eggs.

Non-Vegetarian Filling Ideas: 1) cheese, hashbrown, bacon, chives; 2) cheese, hashbrown, bacon, sausage, green onions; 3) cheese, bacon, sausage

Unbaked savory egg cups in a muffin tin with fillings like bacon, hash browns, and green peppers visible in crepe cups.

Unbaked breakfast egg cups with bacon, sausage, hash browns, and cheese in muffin tin before baking.

Then, pour the eggs into each muffin cup over the fillings. Top with more cheese if desired.

Pouring broth into baked egg cups topped with jalapeños and cheese in a muffin tin.

Baked egg cups in a muffin tin with pasta, cheese, and toppings being filled from a white bowl.

Place in the oven and bake for 20-25 minutes, or until the eggs are set.

Serve: Let the egg cups cool slightly, then carefully remove from the muffin tin. Top with your choice of salsa, avocado, sour cream, or fresh herbs.

Muffin tin of baked egg cups being removed from oven, person wearing red sleeve holding tray.

Baked egg cups in a muffin tin, golden and set, some topped with green herbs and garnishes.

Other Filling Ideas

Eggs: You could add in some milk, half and half (10%) cream, sour cream, or cottage cheese to make the eggs creamier.
Mushrooms
Corn
Tomatoes
Black beans
Spinach
Broccoli
Zucchini
Herbs: Cilantro or parsley
Pepperoni
Diced ham

For Topping

Avocado chunks or slices
Pico de Gallo
Salsa Criolla
Tomatillo Salsa Verde
Refried beans
Guacamole
Hot sauce
Parmesan cheese

Storing Tortilla Breakfast Egg Cups

Of course these Baked Tortilla Egg Cups will taste the best when they’re fresh out of the oven, but that may not be why you came to this recipe! They are indeed super easy to make in advance and keep well in the fridge, but trust me, they are absolutely delicious when they’re hot and freshly baked! To make these in advance, here’s what you need to store them: simply transfer them into an airtight container and store in the fridge. Your vegetarian Breakfast Egg Cups may last a bit longer than the meat options simply because you don’t have to worry about the meat spoiling. However, since these are cooked eggs plus we have cheese, I wouldn’t keep your vegetarian Baked Egg Cups for longer than 5 days, and no more than 4 days for the meat ones.

Baked tortilla egg cups on a white plate, filled with scrambled eggs, herbs, and meat pieces.

How to Reheat Baked Tortilla Egg Cups?▼

If you need to eat your Baked Tortilla Breakfast Egg Cups first thing in the morning - which is probably what you’re looking for in the first place by making this recipe! You should only require about 30 seconds up to 1 minute to reheat your egg cups in the microwave. Keep a close eye on them to ensure they don’t overheat!

Other Eggcellent Starts to the Day!

Fresh and Tangy Egg Toast

Let me know what you think of this recipe in the comments! If you’ve tried this recipe, be sure to post it on social media and tag it with #cookingwithanadi and mention me @cooking.with.anadi. Thank you!

Recipe by Anadi Misra