Healthy Breakfast Casserole | Low Carb Keto-Style

This healthy breakfast casserole is an enchilada-style meal using low carb tortillas filled with scrambled eggs and sausage then topped with a gooey cheese sauce!

Healthy breakfast casserole in a baking pan

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. Have you gotten in the habit to pick around bready dishes to avoid extra carbohydrates?

If so, then you will be thrilled to know 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!


healthy breakfast casserole dish filling in a skillet

Healthy Breakfast Casserole For Keto Followers

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

Hello Keto followers! This is the perfect meal for ya!

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.

Do you see all that cheese? It’s a delicious addition. You can also add avocado cream sauce. YUM.

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

Healthy breakfast casserole filling in a low carb tortilla

Breakfast Casserole Recipe Tips!

This healthy breakfast 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 enchilada style wraps made into a healthy breakfast casserole on a white plate.
Baking pan with low carb tortillas wrapped in eggs and sausage with a melted cheese sauce on top

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.
5 from 10 votes
Print Pin Rate
Course: Low Carb
Cuisine: American
Keyword: brunch, casserole, eggs, keto, low carb
Prep Time: 15 minutes
Cook Time: 20 minutes
Total Time: 35 minutes
Servings: 6 servings
Calories: 751kcal
Author: Sandra @ The Foodie Affair


  • 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


  • 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. 


  • 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 


Serving: 1g | Calories: 751kcal | Carbohydrates: 6g | Protein: 38g | Fat: 63g | Saturated Fat: 30g | Polyunsaturated Fat: 26g | Trans Fat: 1g | Cholesterol: 396mg | Sodium: 1426mg | Sugar: 2g


Please note that the nutritional information provided are guidelines and may vary based on the brand of products used. For your specific nutritional goals use My Fitness Pal or Verywell Fit recipe calculators. All content within this site is not intended as medical diagnosis or treatment and should not be considered a substitute for professional medical expertise.

A white plate with two breakfast filled tortillas on a white plate


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

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  1. 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!!

  2. 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!

  3. 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.

  4. 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!

    1. 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!