Healthy Breakfast Casserole | Low Carb Keto-Style Recipe

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This healthy breakfast casserole is an enchilada-style meal using low carb tortillas filled with scrambled eggs and sausage!


Baking pan with low carb tortillas wrapped in eggs and sausage with a melted cheese sauce on top

Healthy Breakfast Casserole

Everyone has a different interpretation of HEALTHY.  I get that.  Let me tell you why this is one of the best breakfast casseroles for low carb and keto diet followers.

First of all, this dish is made with low carb tortillas, so if you have made it a habit to pick around bready dishes to avoid extra carbohydrates, then you will be thrilled that the tortillas in this recipe are only 3g net carbs each!

Regular tortillas range from 13 to 30 carbohydrates each, so the fact that brands are now making convenience foods that meet our low carb preference is a GAME CHANGER!



Scrambled eggs with sausage and cheese sauce in a skillet for healthy breakfast casserole dish


Also, flavorful meals are hands down the most satisfying and this casserole is filled with tasty ingredients; sausage, egg, and cheese sauce.

Plenty of fat and protein that will keep you full for hours, so you won’t be tempted to snack between meals.

Finally, this is a healthy breakfast that can be enjoyed by the whole family!  Even if the rest of your family are not low carb followers, they’ll enjoy this casserole. Promise!

In fact, I bet they won’t even notice that this meal is anything but delicious!


A tortilla flat on a dark baking sheet with scrambled eggs and sausage in the center


This casserole can be made in advance, but I would add the cheese sauce right before putting it in the oven.

In addition, ensure the casserole dish is tightly covered to prevent the tortillas from drying out.

Try this rehydration hack if they do get a little hard by taking a pasty brush dipped in water and lightly coat each tortilla.

You also might want to give these brunch casserole recipes a try!


Two rolled burritos filled with egg and sausage topped with melted cheese on a cream plate.


5.0 rating
8 reviews

Healthy Breakfast Casserole | Low Carb Keto-Style

This is the best breakfast casserole recipe for low carb and keto diet followers. Hearty and filling enchilada-style dish with scrambled eggs, sausage rolled in low carb tortillas, then topped with a cheese sauce.


  • 1 pound sausage
  • 2 tablespoons butter
  • 8 large eggs, beaten
  • salt and pepper to taste
  • 2 tablespoons butter
  • 1/4 cup minced onions
  • 1 cup milk
  • 2 cups sharp cheddar cheese, shredded
  • 1 tablespoon arrowroot

6 low carb tortillas 


In a large skillet cook sausage* over medium-high heat, breaking up sausage into small pieces.  Remove from pan and set aside. 

Turn heat to medium and add butter to skillet.  Add eggs seasoned with salt and pepper.  Cook for about a minute or until eggs begin to set on the bottom.  Gently pull the spatula across the pan several times while cooking.  Remove from heat and fold in sausage and 1 cups of cheese sauce.

To prepare cheese sauce, in a small saucepan melt butter on medium heat.  Add onion and saute until fragrant and soft.  Add milk and begin adding cheese one cup at a time.  In a small bowl combine arrowroot with 1 tablespoon of water.  Add to cheese and stir until until all cheese is melted and warm (approximately 5 minutes).

To assemble casserole, add about 1/3 - 1/2 cup of egg mixture in the center of each tortilla and roll.  Place filled tortillas seam side down in a lightly greased baking dish. Pour cheese sauce over tortillas and bake for 20-25 minutes.  Top with diced tomatoes. 


Recipe Notes

  • Use your favorite seasoned sausage.  You can also use part bacon and part sausage. 
  • Egg mix is enough for eight.  The photos shows six tortillas in an 8" x 8" baking pan. 
  • I used La Tortilla Factory Low Carb Fajita whole wheat tortillas 
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A white plate with two breakfast enchiladas covered in a cheese sauce


Baking pan with tortillas wrapped in eggs and sausage with a melted cheese sauce on top

Sandra @ The Foodie Affair

13 Comments on Healthy Breakfast Casserole | Low Carb Keto-Style Recipe

  1. February 1, 2018

    I’m all for trying out different ways to be healthier. I hate diets that remove all of life’s little pleasures, so this one is a winner for me. It does look very tasty.

    5.0 rating

    • February 1, 2018

      When you take away my favorite things, that’s ALL I think about! This is a great weekend breakfast meal.

  2. shelby says:
    February 1, 2018

    This looks incredible Sandra! I see the tortillas you have in your post in my grocery and have a package in my freezer. I bought them, then decided not to eat them right away. I have pretty much eaten no “bready” type thing since doing Keto. It’s amazing how you don’t crave it as much when you haven’t had it in so long. I might feel like I’m cheating when I eat one. LOL I have to try this though for brunch one weekend soon!

    • February 1, 2018

      I’m with you! Most times I don’t crave anything bready. I won’t eat low carb tortillas on a regular basis, but once in awhile this is perfect! I’m so glad you are having wonderful success with the Keto diet!! You look so wonderful!

  3. Pam Greer says:
    February 1, 2018

    I love all the yummy ingredients in this!! I agree it would keep me full for hours! Just what I want for breakfast! I don’t necessarily do low carb, so I might use regular tortillas.

    5.0 rating

    • February 1, 2018

      Yes, totally adaptable to any preference. I like whole wheat, but my husband likes regular tortillas so half and half works out great for us!

  4. Angela says:
    February 3, 2018

    I never thought to make a breakfast like this one and now I NEED to make it for my family! I love the tortillas you used!! I use them all the time for taco night!

    5.0 rating

  5. michele says:
    February 3, 2018

    We really enjoyed these– -but we had them for dinner! My husband has already asked for them again!

    5.0 rating

  6. Debra C. says:
    February 3, 2018

    I will be on the look-out for these tortillas. I have eaten their regular, but never tried the low carb, can’t wait to now! Your recipe looks amazing, perfect for any meal!!

    5.0 rating

  7. Julie says:
    February 4, 2018

    I’d love this casserole on my table. It would be perfect for company too!

    5.0 rating

  8. February 5, 2018

    I cannot get over how delicious looking these are — and low carb?? Amazing!

    5.0 rating

  9. Madi says:
    February 7, 2018

    This looks like such a tasty breakfast! I’m all for easy breakfast casseroles!

    5.0 rating

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