Breakfast Muffins Recipe | Jalapeno Popper Eggs - Low Carb / Keto (2024)

This post may contain affiliate links. We receive a small commission at no cost to you when you make a purchase using our links. Please see our Privacy Policy for more details.

Jump to Recipe

This recipe for Breakfast Muffins is a healthy breakfast twist on the Jalapeno Popper appetizers that everyone loves. They are easy to make ahead with cheese, bacon and jalapeño peppers and perfect for busy mornings. Jalapeno egg muffins are packed with protein, low carb and keto friendly.

Breakfast Muffins Recipe | Jalapeno Popper Eggs - Low Carb / Keto (1)

PIN HERE for later and follow my boards for more recipe ideas

With all the egg recipes we have on our site, you guys KNOW that eggs are a big favorite at our house.

Hard boiled eggs, baked eggs, sunny-side up eggs, Frittatas, egg casseroles and of course, these viral Breakfast Muffins that were Pinterest’s top 2018 most pinned egg recipe according to the Today Show and Cooking Light.

These healthy Breakfast Muffins come together quickly in less than 30 minutes and would be perfect for spring.

Breakfast Muffins Recipe | Jalapeno Popper Eggs - Low Carb / Keto (2)


Egg muffins are scrambled eggs that you bake in muffin tins. They are sort of like mini egg omelettes that you can customize with various add-ins and toppings.

They take less than 10 minutes to prep and are full of protein and vitamins.

Plus, they make a delicious make-ahead breakfast that you can quickly reheat on those busy mornings.

What I love about these Jalapeno Popper Breakfast Muffins is that they are the perfect bite-sized breakfast that you can grab on the go.

Plus, they are super versatile and perfect to keep on hand in your fridge or freezer throughout the week.

Bake a batch on your Sunday or Monday meal prep day, wrap them up and store them in the freezer. When you’re ready to serve, grab one of those single mini muffins (or two) and give it a quick reheat and you’re set to go!

And the best part? These keto egg cups are full of protein and super easy to customize. They are naturally gluten free, paleo and low carb.


You can find all our favorite breakfast egg muffin recipes here:

  1. Broccoli Egg Muffins
  2. Buffalo Chicken Egg Muffins – Whole30 / Paleo
  3. Muffin Tin Eggs with Ham and Cheese
  4. Kimchi Egg Muffins
  5. Bacon Egg Muffins
  6. Spinach Egg Muffins
  7. Sun-Dried Tomato and Spinach – Whole30/Paleo
  8. – Whole30/Paleo

Breakfast Muffins Recipe | Jalapeno Popper Eggs - Low Carb / Keto (3)


Breakfast Muffins Recipe | Jalapeno Popper Eggs - Low Carb / Keto (4)

  • eggs
  • salt & black pepper
  • garlic powder
  • onion powder
  • cream cheese
  • cheddar cheese
  • Jalapeno peppers
  • cooked and crumbled bacon


  1. Start off by whisking together your eggs in a 4-cup measuring cup or a mixing bowl and seasoning them with salt, pepper, garlic powder and onion powder. Stir in cream cheese, cheddar cheese, Jalapeno peppers and bacon.
  2. Divide evenly among muffin cups (about 1/2 – 2/3 cups full). Top with one sliced Jalapeno pepper.
  3. I like lining my muffin tin with these silicone liners since they are guaranteed to pop out easily without sticking. If you don’t have silicone liners, be sure to grease the muffin tins with a non-stick cooking spray.Breakfast Muffins Recipe | Jalapeno Popper Eggs - Low Carb / Keto (5)
  4. Pop these in the oven at 400 F and once cooled, you can store them in resealable bags or glass containers. Keep them in the fridge (or freezer) and every morning, heat one up in the microwave for 30-40 seconds. Breakfast is ready to go!
  5. With a batch of these tasty egg muffins, you’ve got a healthy breakfast when you’re on the run each morning.


  • Grease or line your muffin pan with silicone liners for easy removal
  • Fill each muffin cup about 1/2 – 2/3 full
  • Use your favorite combo of vegetables or protein – be sure to chop them up into bite-sized pieces

Feel like switching things up? Here are 9 different Breakfast Egg Muffins you can make instead.

Breakfast Muffins Recipe | Jalapeno Popper Eggs - Low Carb / Keto (6)


For an easy breakfast meal prep recipe, make a batch of egg muffins and store them fridge in a large zip-lock bag or an air-tight container for up to 4 days.


Yes! If you’re wondering how to freeze egg muffins, you would place them in a large zip-lock freezer bag or an air-tight container. You can store egg cups in the freezer for up to 3 months.


To reheat egg muffins in the morning, simply take an egg muffin from the fridge or freezer. Place on a plate and reheat in the microwave on high for about 30 seconds.

You can also reheat the egg muffins in the air fryer or your oven at 375 F for about 5 minutes.

Breakfast Muffins Recipe | Jalapeno Popper Eggs - Low Carb / Keto (7)

More easy egg recipes you might like:

Avocado Egg Cups – Low Carb, Keto, Paleo

Baked Egg Cups – 9 Ways

5 from 5 votes

Breakfast Muffins Recipe | Jalapeno Popper Eggs - Low Carb / Keto (8)


Jalapeno Popper Egg Muffins

Prep Time

5 mins

Cook Time

15 mins

Total Time

20 mins

Jalapeño Popper Egg Cups are an easy make ahead breakfast for on-the-go made with cheese, bacon and jalapeno peppers. Packed with protein, low carb and keto friendly. A healthy twist on the classic appetizer and perfect for busy school or work mornings.

Course: Breakfast

Cuisine: American

Keyword: breakfast, breakfast egg muffins, eggs, jalapeno popper, keto, low carb

Servings: 12

Calories: 113 kcal

Author: Kelly


  • 10 large eggs
  • 1 - 1 1/2 teaspoons sea salt , or to taste
  • 1/4 - 1/2 teaspoon black pepper , or to taste
  • 1/2 teaspoon garlic powder
  • 1/2 teaspoon onion powder
  • 3-4 Jalapeño peppers , de-seeded and chopped plus round slices for topping (if desired)
  • 1/3 cup softened cream cheese
  • 1/2 cup grated cheddar cheese
  • 1/3 cup cooked & crumbled bacon


  1. Preheat oven to 400 F. Line a 12 count muffin pan with silicone liners or coat with non-stick cooking spray. Set aside.

  2. In a large 4 cup measuring cup or mixing bowl, crack in eggs and whisk together with salt and black pepper.

  3. Whisk in garlic powder, onion powder and cream cheese until combined. Stir in cheddar cheese, chopped jalapeño and bacon. Divide evenly into muffin cups filling each about 2/3 full.

  4. Place 1 round jalapeño slice on top in each muffin cup, if desired. Bake in preheated oven for 12-15 minutes, or until set.

Nutrition Facts

Jalapeno Popper Egg Muffins

Amount Per Serving (1 egg muffin)

Calories 113 Calories from Fat 63

% Daily Value*

Fat 7g11%

Carbohydrates 4g1%

Protein 6g12%

* Nutrition facts are provided as a courtesy using the WPRM recipe calculator. It is best to make your own calculations to ensure accuracy. We expressly disclaim any and all liability of any kind with respect to any act or omission wholly or in part in reliance on anything contained in this website. Percent Daily Values are based on a 2000 calorie diet.

Breakfast Muffins Recipe | Jalapeno Popper Eggs - Low Carb / Keto (9)Did you try this recipe?

I'd love to see! Just snap a photo and hashtag it #LIFEMADESWEETER or tag me @lifemadesweeter on Instagram

Breakfast Muffins Recipe | Jalapeno Popper Eggs - Low Carb / Keto (10)

Free Low Carb / Keto Recipes E-Book!

Sign up now to get a FREE low carb / Keto-friendly recipe e-book, plus access to subscriber exclusives!

Breakfast Muffins Recipe | Jalapeno Popper Eggs - Low Carb / Keto (2024)
Top Articles
Latest Posts
Article information

Author: Jerrold Considine

Last Updated:

Views: 5960

Rating: 4.8 / 5 (78 voted)

Reviews: 85% of readers found this page helpful

Author information

Name: Jerrold Considine

Birthday: 1993-11-03

Address: Suite 447 3463 Marybelle Circles, New Marlin, AL 20765

Phone: +5816749283868

Job: Sales Executive

Hobby: Air sports, Sand art, Electronics, LARPing, Baseball, Book restoration, Puzzles

Introduction: My name is Jerrold Considine, I am a combative, cheerful, encouraging, happy, enthusiastic, funny, kind person who loves writing and wants to share my knowledge and understanding with you.