Southwest Black Bean Egg Muffins

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Southwest Black Bean Egg Muffins packed with eggs, black beans, red pepper, onion, and a touch of jalapeno for a spicy and hearty egg muffin that's only 75 calories! Make them on the weekend and eat them all week for breakfast.

151 CAL 13g CARBS 7g FAT 12g PROTEIN 0

Black Bean Egg Muffins are a protein and fiber filled breakfast or snack that can be made ahead of time and enjoyed all week long. These healthy egg muffins are packed with veggies, hearty black beans, and the perfect amount of spice. You;ll also love these Cottage Cheese Egg Muffins and Ham and Cheese Egg Muffins.

We are all about portable breakfasts, especially for super busy weekday mornings. You know the ones I mean when the entire house is chaotically trying to get ready for work and school at the same time. There is nothing better than being able to reach into the fridge on those days and grab a healthy breakfast that's already ready.

Plus these egg muffins are super versatile. You can pop them in the microwave if you prefer it warm, smush it between an English muffin with some avocado or cheese for an on-the-go sandwich, or throw some in lunchboxes for a quick and healthy lunch.

The other great thing is that it is easy to make different flavors in one batch. You can please each and every family member without having to make ten different breakfasts.

How to Make Egg Muffins

Breakfast egg muffins are one of my favorite breakfast meals. You can make endless combinations and they are filling and portable. To make twelve muffins, I usually use either 12 whole eggs or a combination of 8 egg whites and 4 whole eggs for a lighter version. Then I add in veggies, lean protein sources, and cheese. It's up to you whether you cook the veggies beforehand, but I find they come out better if you do.

Here's the base recipe:

  • 12 eggs
  • 1 cup fillings (cooked veggies, lean protein)
  • 1/2 cup cheese
  • Salt and pepper
  • Directions: Preheat the oven to 350 degrees. Spray the muffin tin with cooking spray. Whisk the eggs until combined. Season with salt and pepper. Stir the fillings into the eggs. Divide evenly among the muffin tin. You can also fill the bottoms of the muffin tins with the fillings and pour the eggs over top. Bake for 20-25 minutes until cooked through. Wait 5-10 minutes before removing them from the tin.

For this version, I decided on a combination of black beans, peppers, and red onion. I left out the cheese since I am trying to cut back, but some shredded cheddar or goat cheese would be deliciously mixed in. You will notice that this version has fewer eggs than the standard recipe. That's because I wanted to use more black beans. If you want to use mor fillings, you may need to scale back on the eggs.

Healthy Egg Muffins with black beans, red peppers, onion, and jalapeno.

The other thing I love about this particular egg muffin recipe is that the black beans add fiber and filling power. While some egg muffins may leave you hungry a few hours later, these muffins have more staying power. You can use any bean you like, but I am partial to black beans for Southwestern inspired recipes. Sometimes I also throw in some taco seasoning as well to really kick up the flavor combination.

Recipe Ideas for Black Bean Egg Muffins

  • Looking for extra protein? Add in some chopped deli ham or turkey. Cheese is also a great way to add protein. Consider using cheddar, goat cheese, or pepper jack for some extra spice.
  • Kick up the nutrition! These muffins can handle all kinds of veggies. Add spinach, mushrooms, corn, zucchini, or tomatoes.
  • More taco flavor? Consider adding some taco seasoning to the eggs to pack in even more flavor.
  • Too much heat? Leave out the jalapenos or just use a tiny amount.
  • Have kids? Kids love these muffins and it's a great way to sneak in some extra veggies. They taste great warm or cold and make a great lunch item or afternoon snack.
  • Have leftover egg muffins? Warm up some corn tortillas and make delicious breakfast tacos.

Egg Muffins packed with black beans, veggies, and a touch of heat.

Tips for Making Egg Muffins

  • Always make sure to spray the muffin tin with cooking spray. These will stick if you skip this step.
  • For the best results, always sauté your veggies beforehand. That way you guarantee you won't have a super crunchy veggie in your egg muffin.
  • If you don't have time to cook your veggies, use defrosted frozen veggies or canned vegetables that are already soft.
  • Let the egg muffins rest for at least 5 minutes before removing them from the pan. They will come out much easier.
  • These will puff up when they are cooking, so make sure to only fill the muffin tin about 3/4 of the way up.
  • Feel free to mix up the flavors in a single batch. Just add the individual toppings to the bottom of the muffin tin and pour the eggs over top. Consider making a row for each family member.

Here are some tools that helped when I was preparing this recipe:

  • Muffin tin: Although I used a metal muffin tin for the photos, usually I reach for a silicone muffin tin for making egg muffins since they stick the least. It almost guarantees that your muffins will pop right out after cooking. If not, you may want to use paper liners for the muffins.

This recipe originally was posted in 2014 but has been updated with new photos, tips, and ideas for cooking.

Common Egg Muffin Questions

We try to give you all the information you'll need for this recipe, but here are a couple of additional questions with their answers just in case.

Cooked egg muffins will last 4-5 days in an airtight container. They can be eaten cold, room temperature, or can be reheated in the microwave. These cook quickly and generally only need 10-15 seconds to reheat.

These are a great option for the freezer and will last 2-3 months. Start by letting the cooked egg muffins cool completely. Then place them on a baking sheet and place them in the freezer for 2 hours. This will freeze the outside of the muffin so they don't stick together. Now just add them to a freezer safe container.

The Recipe
Black bean egg muffins in a muffin tin with eggs, black beans, and red pepper on the side.

Southwest Black Bean Egg Muffins

151 CAL 13g CARBS 7g FAT 12g PROTEIN 0
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  • 1.5 cups canned black beans, drained and rinsed
  • 1 green bell pepper, diced
  • 1 jalapeno, seeded and diced
  • 1/2 cup red onion, diced
  • 8 large eggs
  • Salt and pepper

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Preheat the oven to 350 degrees.


Spray a nonstick skillet with cooking spray. Add the peppers, onion, and jalapeno if using and cook until tender, about 6-8 minutes.


Meanwhile, whisk together the eggs. Season with salt and pepper.


Add the peppers, onions, and black beans to the eggs.


Spray a muffin tin with cooking spray. Pour in the egg mixture.


Bake for 20-25 minutes until puffed up and cooked through.

Nutritional Facts
Serving Size: 2 muffins
Amount Per Serving
Calories 151
Calories from Fat 59
% Daily Value *
Total Fat 7g
Saturated Fat 2g
Monounsaturated Fat 0g
Polyunsaturated Fat 0g
Cholesterol 248mg
Sodium 326mg
Total Carbohydrate 13g
Dietary Fiber 5g
Sugars 2g
Protein 12g

* Percent Daily Values are based on a 2,000 calorie diet. Your daily values may be higher or lower depending on your calorie needs.

The Nutritional Values provided are estimates only and may vary based on the preparation method.

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About the author Meet Kristen McCaffrey
Hi, I’m the cookbook author, recipe developer, and food enthusiast behind Slender Kitchen. I am obsessed with making healthy food that is easy to prepare and absolutely delicious. Meal planning is my secret weapon and I hope I can make meal time easier for you with our tried and tested recipes and foolproof meal plans. Learn More
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On Southwest Black Bean Egg Muffins
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December 19, 2023 - 10:44
Add a Rating:
Love these and your other recipes can't wait to make those too!
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Donna Dosh Speer
July 26, 2023 - 11:12
How many muffins for one recipe?
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September 19, 2023 - 09:28
It makes 12 standard sized muffins.
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Sarah Ocampo
July 13, 2022 - 15:08
Add a Rating:
I've made muffin tin quiches before, but never thought to add beans! I didn't have jalapeno on hand, so added some shredded zucchini instead. Yum! This will be a good breakfast and/or snack for the whole family.
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Blade L Hale
September 14, 2021 - 06:04
Add a Rating:
ehem.... beans
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Linda McDonell
September 7, 2018 - 13:31
Add a Rating:
I've made these a million times a million different ways. I'm making a pizza version today but have gone southwestern, hot with jalapenos, bacon, ham etc etc. Every time we hit the road in our RV I make a few dozen and freeze for quick on the go breakfasts!
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January 29, 2019 - 10:31
Yum!! I may have to copy you and try that pizza version. Sound so good!!
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Nicole Biette
July 22, 2018 - 10:39
These were easy to make ahead and freeze!
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January 29, 2019 - 10:31
So glad you enjoyed them! We love having a big batch in the freezer as well.
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Megan Eaton
March 4, 2016 - 10:46
Add a Rating:
Really liked this recipe. I added in some cheese, but definitely a good breakfast!
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January 29, 2019 - 10:32
I love adding cheese as well! It makes everything taste better :) Lately we have been making them with goat cheese and it's delicious.
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February 26, 2016 - 14:21
I pinned it anyway, but there seems to be a picture missing! So you need to make these and take a pic (and if you want to air mail them to me, that'd be great! ;) )
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January 29, 2019 - 10:32
That's strange! Hopefully, you are able to see the picture now :) I would totally airmail them if I could.
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