The Ultimate Guide to Breakfast Egg Cups

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Cooking With Anadi

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It’s back to school season and that can mean some really busy mornings. However, I really hate it when people neglect breakfast! Personally, I think it’s really important to have a hearty and nutritious breakfast, as it can really give you energy and set you up for success! That’s why prepping a healthy breakfast is key to ensure you don’t go for some “bad” choices at fast food joints, where those items are totally processed! Don’t get me wrong, I love breakfast sandwiches from McDonald’s and similar breakfast joints, but they do tend to make me feel lethargic and heavy, plus the money spent on those adds up! Save some money and enjoy a healthy breakfast by making these Baked Egg Cups for Breakfast! To recreate that coffee shop experience at home, be sure to pair these Tortilla Egg Cups with a hot drink, such as a French Vanilla Cappuccino or Turmeric Chai Latte.

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!

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!

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!

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 molds.
• While you can pick whichever order to prepare the fillings for the egg cups, my favorite ones were where I had cheese at the bottom and the top of the egg cups.
• Try 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 molds.
• 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.

Tools Needed to Make Baked Egg Cups

• Salt crock
• Pepper mill
• Whisk
• Cutting board
• Chef’s knife
• Measuring cups or large mixing bowl
• Olive oil spray bottle
• Muffin pan

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.

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 “pulliness” plus flavor, 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.

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 favorite. You’ll want to dice them.
• Green onions
• Chives

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 Chili 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.

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.

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

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

Pick whichever filling options from below and prepare the tortillas:

For the Vegetarian Breakfast Egg Cups

Vegetarian Filling Ideas: 1) cheese, chives, jalapeño; 2) cheese, green onions, hash brown pieces; 3) peppers, onions, jalapeño, cheese; 4) peppers, onions, hash browns, cheese, chives

For the Meaty Egg Cups

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

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

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.

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.

What to Serve With Breakfast Egg Cups

These egg cups are hearty enough to stand on their own, but they are even better as part of a bigger spread. For a balanced, filling breakfast, pair a couple of cups with fresh fruit or a handful of berries, some avocado toast, or crispy breakfast potatoes. A green smoothie or a glass of juice rounds things out on a busy morning, and of course a good cup of coffee never hurts. Because each cup is already loaded with eggs, cheese, and your choice of fillings, one or two alongside a light side is usually all you need.

Are Tortilla Breakfast Egg Cups Healthy?

There is a lot to love here nutritionally. Each cup is built on eggs, so they are naturally high in protein to keep you full through the morning, and baking them in a muffin tin means built-in portion control. The corn tortilla base is a whole-grain, gluten-free swap for a heavier pastry crust, and you can pack in as many vegetables as you like — bell peppers, onions, jalapeños, green onions, and chives all work beautifully. Keep them fully vegetarian, or add sausage and bacon for a heartier version; either way, you control exactly what goes in. Top with avocado or salsa instead of extra cheese for a lighter finish.

Other Egg-cellent Starts to the Day!

• Egg Soufflé For One
• Bacon, Egg and Guacamole Bagel
• Breakfast Bagel BELT
• Fresh and Tangy Egg Toast

Muffin Pan Size, Egg Count and Scaling the Batch

The recipe is built around a 12-cup muffin pan, 12 small corn tortillas and 10 large eggs, which is why it makes a dozen cheese tortilla cups in one go. Ten eggs across twelve muffin tin cups sounds like it should not stretch, and it just about does, which is why the ingredient list says to use more eggs if needed. Crack them into a large bowl or measuring cup, season with salt and pepper, and pour the egg mixture over the fillings in each cup until they are roughly three-quarters full. Leave a little headroom, because the eggs puff as they set at 350F and will spill over the rim if you fill them to the top.

If all you own is a 6-cup muffin pan, nothing here breaks. Either halve everything and use 6 tortillas with 5 eggs, or keep the full quantities and bake in two batches back to back, since the oven is already hot and each batch only needs 20 to 25 minutes. A 24-cup mini muffin pan works as well, though the cups bake considerably faster, so start checking them at around 12 minutes and use the shake test the tips section describes rather than the clock.

On seasoning, there is no measured tsp of anything in this recipe. Salt and pepper are listed to taste, and that is deliberate, because how much you need depends entirely on whether you have gone the veggie route or loaded the cups with bacon and sausage, both of which are already salty. Season the eggs in the bowl rather than each cup, taste as you go if you are comfortable doing that, and sprinkle a little extra shredded cheese over the top before they go in the oven.

Two easy additions that are not part of the recipe as written but sit comfortably alongside it. A small spoonful of cream cheese dropped into the bottom of each cup melts into the eggs and gives you a richer, creamier set, in the same spirit as the sour cream and cottage cheese already suggested above. And if you are making these for brunch rather than a weekday morning, bake them in two staggered batches so the second tray is coming out of the oven just as people sit down, since these really are best hot.