Add a little zest to your breakfast with green chiles, corn tortillas and melted cheese. This baked egg dish is cooked quick and easy in less than 3 minutes.

Table of Contents
Incredible Baked Eggs
I’ve started a new job and with it comes a 30-45-minute commute. I am not a morning person, so getting up early to prepare a healthy breakfast first thing in the morning is not on my agenda. Instead, I’ve been experimenting with ways to make quick microwave breakfasts packed full of protein and flavor.
I have these great little Le Creuset Mini Cocottes that are so cute and the perfect-sized baking dish for breakfast on the go. They’re microwave and oven-safe. I’ve been using them almost every day to make individual bread pudding, Croque Madame and now these egg stacks.
If you don’t have mini cocottes, you can use regular 7-oz. ramekins instead, but you’ll need to cover the ramekin with a plate when it’s in the microwave because eggs love to explode.
I tried this recipe 6 different ways because I wanted runny yolks and firm egg whites, but you know what? It didn’t need a runny yolk. The green chiles, corn tortillas and wonderfully melted cheese give this dish enough zest and goodness.
What makes this Zestuous breakfast even better is that you can prepare these egg cups in advance and pop them in the microwave when it’s time to eat.
This recipe is also great for special occasions where you’re entertaining company because, if your guests are anything like mine, they never all wake up at the same time.
Just meal prep a batch of the mini cocottes in advance and everyone can heat their own when they’re hungry.

Baked Eggs in the Microwave with Green Chiles
Ingredients
- 12 corn tortillas, street taco size
- cooking spray
- 4 oz can chopped green chiles
- 4 eggs
- 1 tomato , sliced
- 4 slices Sargento Ultra-thin colby jack cheese
- pinch Kosher salt
- pinch black pepper
- pinch ground cumin
Instructions
- Prep: Cut each tortilla into a 3-inch round using a cookie cutter or cup.
- Spray: Grease the cocotte or ramekin with cooking spray.
- Layer 1: Add a tortilla round and spray again. Add one tablespoon of green chiles on top.
- Layer 2: Place another tortilla round on top and spray again.Crack an egg on top.
- Layer 3: Add another tortilla round on top. Spray again. Add a tomato slice and a slice of cheese on top.
- Cook: Cover and microwave for 1 minute and 15 seconds.
- Plate: Enjoy straight from the ramekin. Or, run a rubber spatula or spoon around the edges of the baked egg stack and transfer it onto a plate.
- Season: Add a pinch of salt, pepper and ground cumin to taste.
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.

Ingredients for a Southwestern breakfast stack
- Yellow Corn Tortillas. I love the color and texture of these, but you can use flour tortillas here too. Look for the street taco size tortillas.
- Cooking Spray
- Diced Green Chiles. You can find these in small cans in the Hispanic food aisle at your local grocery store.
- Large Eggs
- Fresh Tomato
- Colby Jack Cheese. I keep Sargento Ultra Thin slices on hand for this recipe.
- Kosher Salt
- Black Pepper
- Cumin: This spice makes all the difference.
Substitutions: There are so many pepper options to choose from. You can use spicy or mild green chiles, hatch green chiles, chile rellenos or even chopped poblano peppers. Feel free to use different kinds of cheese too, sharp cheddar, Monterey jack cheese or pepper jack cheese would all be delicious here.
See the full recipe card for servings and a full list of ingredients.
How to make mini egg breakfast casseroles
- PREP: Cut each tortilla into a 3-inch round using a cookie cutter or cup.
- SPRAY: Grease the cocotte or ramekin with cooking spray.
- LAYER 1: Add a tortilla round and spray again. Add one tablespoon of green chiles.

- LAYER 2: Place a tortilla round on top and spray with cooking spray. Crack an egg on top.

- LAYER 3: Add another tortilla round on top. Spray with cooking spray again. Add a tomato slice then a slice of cheese.


- COOK: Cover and microwave for 1 minute and 15 seconds.

- PLATE: Run a rubber spatula or spoon around the edges of the egg stack and transfer it onto a plate.
- SEASON: Add salt, pepper and ground cumin to taste.
✔️ PRO TIP
To build flavor, sprinkle a little seasoning on each layer.

How to serve baked eggs
Like I said, I love to keep these on hand for those mornings I’m rushing out the door, but they’re also perfect centerpieces for a weekend brunch.
Set out one ramekin per guest and fill your table with toppings like sour cream, hot sauce, red onion and pre-shredded cheese.
Serve alongside Mexican rice and refried beans along with some freshly sliced fruit for your next brunch and watch as your friends fall in love with your cooking.
Storage
Store these in an airtight container in the fridge and they’ll keep for several days. You can also take them out of their dish, wrap them with plastic wrap or place them in a freezer bag and keep them for weeks to pop in the microwave whenever you need a quick bite.
Frequently Asked Questions
Not at all. The eggs cook up beautifully when they’re cooked following this method.
They range in spiciness depending on the type. Look for canned mild green chiles if you’re looking for something with tons of flavor but not as much heat.
Eggs have the same amount of calories no matter if they’re fried, baked or microwaved. If you add fat like butter or oil while you’re cooking them, that’s where you start to increase the fat and calories.
This recipe only calls for some cooking spray, so it is healthier than frying eggs in a skillet of butter.










Thanks so much for your wonderful recipes! I am just starting to learn how to cook, hopefully cook healthy, and I love your site. I’d just like to ask, what could be a good alternative to chilles? I’m not very tolerant of spicy food but I do want that “kick” in flavor.
You’re so welcome Ira. You can buy mild green chiles in the can, but if you think that still might be too much heat, try roasted red peppers. They come in a jar near the pickles. They would still give you nice bold flavor without the heat.
Thank you! I read your reply just when I was at the grocery and found the roasted red peppers just where you said they would be. I was amazed and thankful they were there in a regular supermarket since it’s not always easy to find those kinds of things here in the Philippines. I really appreciate all the help! Keep on writing!
These are a perfect idea for breakfast. I think I have just found a great breakfast menu! Thanks for sharing. I’m sharing this the girls at work!
Thanks! Enjoy!!!