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Home » Recipes » Breakfast and Brunch

Mexican Egg Bake with Beans and Cheese

A picture of Ashlyn Meredith in the kitchen.
Modified: Sep 15, 2025 · Published: Sep 7, 2023 by Ashlyn Meredith · This post may contain affiliate links · Leave a Comment
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This Mexican Egg Bake with Beans and Cheese is made in individual sized ramekins and makes the perfect personal sized hot breakfast. With a refried bean mixture spread on the bottom, a layer of corn tortilla strips, cheddar cheese, and fresh salsa, this is a flavorful and satisfying breakfast or brunch option.

Egg bake in individual ramekins topped with sour cream and cilantro.

If you are looking for a delicious, impressive and filling morning meal, you will love these individual egg bakes. Each bite is packed with flavor, thanks to the refried bean mixture spread on the bottom and the fresh salsa piled on top! Make these when you have overnight guests, for meal prep or anytime you are looking for something a little different to start your day!

This is a great make-ahead breafast that you can prep on Sunday and enjoy throughout the week. Simply pop them in the microwave until they are heated through, top with some of the fresh salsa and sour cream and you are ready to go!

For more delicious breakfast ideas, try: Caramel Pecan Sticky Buns With Orange Zest, Fresh Strawberry Buttermilk Scones with Lemon Zest Glaze or Easy Apple Cider Pancakes.

Jump to:
  • Why You Will Love This Recipe
  • Ingredients Needed
  • Step by Step Instructions
  • Expert Tips
  • FAQ
  • Storing and Freezing
  • Other Recipes to Try
  • Recipe

Why You Will Love This Recipe

  • The fresh salsa. Fresh salsa made with tomatoes, jalapeños, red onion, cilantro, and fresh lime juice adds the most delicious and fresh flavor to this recipe. You will add some to the tops before baking and then can serve with more for topping before eating!
  • It is personal sized. This recipe is baked in four individual ramekins, making them the perfect individually sized breakfast. This also makes it great for meal prep. Make these on the weekend and warm up throughout the week for breakfast.
  • It is filling. The beans, eggs and tortillas help to fill you up and fuel your day. Serve these egg bakes with some fresh fruit and you have a complete meal!
Egg bake in individual ramekins topped with sour cream and cilantro.

Ingredients Needed

Here are notes about some of the ingredients needed to make this easy recipe. All ingredients can be found at your local grocery store or at an online retailer, like Amazon.

  • Tomato
  • Red onion
  • Cilantro
  • Jalapeño: Use fresh jalapeño with the seeds and ribs removed. For added heat, leave the seeds and ribs in!
  • Salt & black pepper
  • Lime juice: Use freshly squeezed lime juice for the best flavor. You will use this in the salsa and in the bean mixture.
  • Garlic: Use garlic in the salsa and the bean mixture. Fresh garlic cloves are always going to have the best flavor but bottled minced garlic is great for convenience.
  • Refried beans: I prefer to use regular refried pinto beans, but you could use refried black beans or mashed beans in place of the refried.
  • Cumin
  • Milk: Feel free to use your preferred kind of milk.
  • Eggs
  • Green onions
  • Tortillas: Corn tortillas provide the best flavor in this dish, but flour tortillas or crushed up tortilla chips would be a great alternative.
  • Cheese: I like to use sharp cheddar cheese, but shredded pepper jack cheese, Mexican blend, or Monterey jack would work great too.
  • Sour cream: Serve with sour cream and fresh salsa. To reduce a few calories, substitute the sour cream for greek yogurt.
Egg bake ingredients in varying bowl shapes and sizes.

Step by Step Instructions

Here is how to make this great dish. You will need four large ramekins and a baking sheet for this recipe. For the full ingredient list and instructions, see the recipe card below.

STEP 1: In a medium sized bowl, combine all of the salsa ingredients. Stir well and set aside.

STEP 2: Preheat the oven to 350°F. Spray four ramekins with cooking spray and place them on a baking sheet.

STEP 3: In a small bowl, combine the beans, lime juice, garlic, and cumin. Stir well to combine.

Egg bake preparation.
Egg bake preparation.

STEP 4: Divide the bean mixture between the four ramekins and spread in an even layer to cover the bottom.

Egg bake preparation in individual ramekins.

STEP 5: Cut the tortillas in half and then into ½-inch strips. Divide the tortilla strips between the four ramekins and then top with the shredded cheese.

Egg bake preparation in individual ramekins.
Egg bake preparation in individual ramekins.

STEP 6: In a large bowl, combine the eggs and milk. Whisk until fully combined. Add the green onions, salt and pepper. Divide the mixture between each of the ramekins by carefully pouring it into each one.

Egg bake preparation.
Egg bake preparation.
Egg bake preparation in individual ramekins.

STEP 7: Tops each ramekin with a spoonful of the fresh salsa.

Egg bake preparation in individual ramekins.

STEP 8: Bake in the preheated oven for 33-35 minutes or until the eggs are set. Serve with a dollop of sour cream, fresh salsa and cilantro as a garnish.

Egg bake in individual ramekins topped with sour cream and cilantro.

Expert Tips

Here are some tips for making this egg cups perfectly each time.

  • Prepare the salsa in advance. The fresh salsa can be stored in the refrigerator for up to 5 days.
  • To use the entire can of refried beans, double the recipe and make enough to have leftovers all week!
  • Serve with hot sauce for extra heat and flavor.
  • Feel free to add in any addtional veggies or seasonings to your salsa that you have on hand. Some good choices may be bell peppers, green chilies, or ground cumin.
  • Serve these egg bakes alongside some hash browns or breakfast potatoes.
Egg bake in individual ramekins topped with sour cream and cilantro.

FAQ

Can I use store bought salsa?

Yes. If you would rather skip the step of making fresh salsa, feel free to use store bought bottled or fresh salsa.

Can I make this without the beans?

Yes. If you would like to make this without beans, just skip that step and have the bottom layer be the tortilla strips.

Can I make these ahead of time?

Sure. If you wanted to you could prepare the salsa and other ingredients the night before and assemble and bake in the morning. Leftover egg bakes are easily warmed up and just as delicious!

Could I make this in one large casserole dish?

Yes. If you would like to make this as one larger egg bake, simple assemble in a square 8x8 or 9x9-inch baking dish. Note that the cooking time may vary, so just keep an eye on it and once the eggs are set in the center, you should be good to go!

Storing and Freezing

Store leftovers covered tightly with plastic wrap in the refrigerator for up to 5 days. Store salsa covered tightly in the refrigerator for up to 5 days.

Egg bake in individual ramekins topped with sour cream and cilantro.

Other Recipes to Try

  • Sliced pork tenderloin on a plate with sweet potatoes and apples.
    Apple Pork Tenderloin
  • Pumpkin blondies with a cinnamon sugar top cut into squares.
    Cinnamon Sugar Pumpkin Blondies
  • A stack of three waffles topped with butter, pecans and a drizzle of maple syrup.
    Pumpkin Pie Spice Waffles
  • A pumpkin bar on a white plate.
    Pumpkin Bars with Graham Cracker Crust

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Recipe

An individual egg bake in a white ramekin topped with sour cream and cilantro.

Mexican Egg Bake with Beans and Cheese

This Mexican Egg Bake with Beans and Cheese is made in individual sized ramekins and makes the perfect personal sized breakfast. With a refried bean mixture spread on the bottom, a layer of corn tortilla strips, cheddar cheese, and fresh salsa, this is a flavorful and satisfying breakfast or brunch option.
5 from 1 vote
Print Pin SAVE Saved!
Prep Time 10 minutes mins
Cook Time 35 minutes mins
Total Time 45 minutes mins
Course Breakfast
Cuisine Mexican
Servings 4
Calories 297 kcal
Keeps your screen on while you cook.

Ingredients
  

For the Fresh Salsa:

  • 1 cup tomato, chopped
  • ¼ cup chopped cilantro
  • ¼ cup finely chopped red onion
  • 1 teaspoon minced jalapeno
  • ½ teaspoon minced garlic
  • ¼ teaspoon salt
  • Juice of 1 lime

For the Egg Bake:

  • 1 cup refried beans
  • ½ teaspoon garlic
  • ¼ teaspoon ground cumin
  • Juice of 1 lime
  • 4 corn tortillas
  • ½ cup shredded sharp cheddar cheese
  • 6 large eggs
  • 1 tablespoon milk
  • 1 teaspoon salt
  • ½ teaspoon black pepper
  • ¼ cup chopped green onion
  • Sour cream, for serving

Instructions
 

For the Salsa:

  • In a medium sized bowl, combine all of the ingredients for the salsa and set aside.
    1 cup tomato, chopped, ¼ cup chopped cilantro, ¼ cup finely chopped red onion, 1 teaspoon minced jalapeno, ½ teaspoon minced garlic, ¼ teaspoon salt, Juice of 1 lime

For the Egg Bake:

  • Preheat the oven to 350°F. Spray four large ramekins with cooking spray and place on a baking sheet.
  • In a small bowl, combine the refried beans, garlic, cumin, and lime juice. Stir well to combine.
    1 cup refried beans, ½ teaspoon garlic, ¼ teaspoon ground cumin, Juice of 1 lime
  • Divide the bean mixture among the four ramekins and spread in an even layer to cover the bottoms.
  • Cut each tortilla in half and then into ½-inch strips. Divdie the strips among the four ramekins and then top with the shredded cheese.
    4 corn tortillas, ½ cup shredded sharp cheddar cheese
  • In a large bowl, whisk the eggs and milk until fully combined. Add the salt, black pepper and green onions. Whisk until combined.
    6 large eggs, 1 tablespoon milk, 1 teaspoon salt, ½ teaspoon black pepper, ¼ cup chopped green onion
  • Carefully divide the egg mixture among the four ramekins. Top each one with a spoonful of the fresh salsa.
  • Bake in the preheated oven for 33-35 minutes or until the eggs are set. Top with fresh salsa, sour cream and cilantro as a garnish, if desired.
    Sour cream, for serving

Video

Nutrition Information

Calories: 297kcal | Carbohydrates: 26g | Protein: 18.6g | Fat: 13.9g | Saturated Fat: 5.8g | Cholesterol: 299mg | Sodium: 546mg | Potassium: 479mg | Fiber: 5.9g | Sugar: 3.2g | Calcium: 204mg | Iron: 3mg

Please note that these nutrition facts are approximations and may not be entirely precise.

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Keyword cheddar cheese, eggs, refried beans, salsa, tortillas
Did you make this recipe?Leave a comment below and tag @heysnickerdoodle on social!

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5 from 1 vote (1 rating without comment)

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An individual egg bake in a white ramekin topped with sour cream and cilantro.

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