30-Minute Gluten Free Enchilada Casserole

If you like gluten free enchiladas, you are going to love this gluten free enchilada casserole! Think all the same enchilada flavors, just without any work of rolling the tortillas! Plus the cassrole is packed with fresh vegetables, melted gooey cheese and has the option to add shredded chicken!

This gluten free enchilada casserole is the ultimate comfort food dish to make instead of ordering in. I hate how long take-oute takes…plus its never warm when it arrives! So cut the at-home take-out recipes! This incredibly easy stove top enchilada casserole is hot and fresh every single time! It is made with all gluten free ingredients so it is a fully gluten free dinner recipe!

I love a one pan meal because honestly, less dishes to clean up! The same is true for my chicken taco rice casserole, my  easy unstuffed pepper skillet and this one pan chicken teriyaki!

why you’ll love this allergy friendly Gluten Free Enchilada Casserole recipe

• This gluten free enchilada casserole comes together quickly, is easy to make and makes for the perfect leftovers or meal prep. I love making this recipe on a sunday night and using the leftovers for weekday lunches.
• I love this recipe because I just add everything to a skillet! Then, I top it with sauce and cheese and let it cook. It takes just a few minutes of effort but you get such a big reward.
• This gluten free enchilada casserole recipe is packed with big enchilada flavor and you can really make it as spicey as you’d like: spicy, medium or mild. I prefer mild…but my husband would say spicy!
• This recipe is perfect for anyone who has dietary restictions or food allergies. It is already naturally gluten free but you can make it dairy free just by using dairy free cheese!

ingredients & substitutions

Vegetables: Butternut squash, Tomatoes, bell pepper, and onion provide the vegetable base for the dish.

Protein: Black beans and optional chicken add protein and substance. You can add anything from shredded chicken to ground chicken or even ground turkey.

Corn Tortillas: Corn tortillas offer a hearty texture and soak up the flavors of the gluten free enchilada casserole. They are in classic enchiladas so you don’t want to skip them in the skillet version unless you need a low carb option! Then I’d skip it!

Enchilada sauce: Enchilada sauce provides the signature Mexican flavor. Not all canned or premade enchilada sauces are gluten-free. They do often contain wheat, so make sure you are checking ALL labels before purchasing. If you cannot find enchilada sauce feel free to use salsa or taco sauce in place.

Cheese: I use shreddded cheddar but you can use any cheese you have from mozzarella to pepeprjack. For a dairy free recipe I use dairy free cheese.

Gluten Free Enchilada Casserole directions

Step 1

In a large skillet, sauté the butternut squash, bell pepper, and onion in a little olive oil until softened, approx 20 minutes on medium low.

Step 2

Stir in the diced tomatoes, black beans, and half of the enchilada sauce. Season with salt and pepper to taste.

Step 3

Tear the corn tortillas into bite-sized pieces and add them to the skillet. Pour the remaining enchilada sauce over the tortillas.

Step 4

Sprinkle the shredded cheese evenly over the mixture. If using chicken, add it now.

Step 5

Cover the gluten free enchilada casserole and cook for about 10 minutes, or until the tortillas are softened and the cheese is melted.

expert tips & tricks

• Feel free to use more cheese! I love a recipe like this when I am really craving a cheesy dish.
• This gluten free enchilada casserole recipe also doubles really easily for a meal prep or a larger crowd. I just make extra layers in your skilet!
• You can make this recipe in a slow cooker, crock pot, instapot or casserole dish. The cook time will just vary.

serving, storing and meal prepping the Gluten Free Enchilada Casserole

I always find this gluten free enchilada casserole is delicious on its own, but I do often serve it with a side of tortilla chips, guacamole, or a simple green salad. 

Leftovers of the recipe store great! I let the casserole cool completely, then place it in an airtight container or covered with aluminum foil in the fridge for up to 3-5 days. I love bringing it with me to work for an easy hot lunch.

For longer storage, I also freeze the gluten free enchilada casserole in individual containers for up to 3 months. 

Reheat leftovers of the skillet in the oven or on the stovetop until warmed through, or thaw frozen portions in the fridge overnight and bake in a preheated oven at 350°F (175°C) until heated through. 

Looking for more allergy friendly easy recipe?

If you make this recipe and enjoyed it, I would really appreciate a review! You can find me on Instagram, Facebook, Tik Tok and Pinterest. Purchase my cookbook Easy Allergy Free Cooking. Join my exclusive weeknight meal plan group for 5 weekly 30-minute dinner recipes. The weeknight meal plan also has an accompanying podcast as well! I would love for you to follow along! 

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