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One of my favorite weeknight meals, this single-skillet chicken fajita casserole is warm, savory, and perfect for using up leftover chicken! Full of fresh vegetables and topped with melty cheese and gluten-free tortilla chips, the entire dish comes together in under an hour for a quick, family-friendly dinner. Dairy-free option, too.

Baked chicken fajita casserole in skillet, topped with melted cheese, diced tomatoes, and cilantro.

Some recipes are born out of “what do I have in the fridge?” moments—and this casserole is exactly that. It’s scrappy, simple, and forgiving (so no stressing if you eyeball the spices or cut your peppers unevenly). Now, full disclosure: this isn’t exactly fajitas—we’re skipping the tortillas—but it is fajita-inspired. The chicken and veggies get that same bold seasoning and skillet sizzle, then everything bakes together under a layer of tortilla chips for crunchy topping. It’s kind of like fajitas met nachos and decided to throw a weeknight dinner party. And honestly? I’m not mad about it.

Lindsay’s Top Tips and Tricks Before You Begin

Spice it your way: If you or your family prefers things on the mild side, use ½ teaspoon of regular chili powder. Or, boost the flavor with extra cumin and paprika for warm depth without all the heat.
Time-saver: Swap the sweet potato for 1 cup of cooked rice or a can of drained black beans, and stir it in with the chicken. The texture changes slightly, but it’s still hearty and delicious.
Skillet alternative: If you don’t have an oven-safe skillet, transfer the filling to a casserole dish, then layer on the chips and cheese before baking.

Ingredients and Notes

Please be sure to scroll down to the recipe card below for the complete details and substitute notes!

Overhead view of ingredients for chicken fajita casserole, including shredded chicken, shredded cheese, green bell peppers, onion, garlic, sweet potato, canned tomatoes, tortilla chips, milk, and spices arranged on a marble surface.

Oil – I use olive oil to sauté the veggies and add flavor to the sauce. For an even richer taste, use dairy-free butter (or plain butter if dairy isn’t a concern) as the base of the sauce.
Veggies – Minced garlic, bell pepper, onion, and sweet potato add color, nutrients, and fiber to the skillet, making it extra filling. Then, I use diced tomatoes with green chiles for the sauce, adding a touch of extra heat.

Ingredient Swap: If preferred, you may use diced peeled squash or russet potato, or 1–1 ½ cups cooked rice or quinoa (stir in when adding the chicken) instead of the sweet potato. You can even substitute cauliflower rice if you want to keep this dish low-carb.

Seasonings – Instead of using store-bought fajita seasoning packets (which can sometimes have gluten), I make a simple homemade blend of chili powder, cumin, paprika, salt, and pepper.

Ingredient Swap: Use ½ teaspoon of garlic powder with the other spices if you don’t have fresh garlic. Then, use regular chili powder for a milder flavor, or bump up the paprika and cumin for depth without too much spice.

Arrowroot Starch or Cornstarch – Whisked with water or broth, this helps thicken the sauce. Arrowroot gives a clear, glossy finish, while cornstarch makes the sauce more opaque. Both work well—just use whichever you prefer.
Dairy-Free Milk or Broth– This helps combine the ingredients. Use full-fat canned coconut milk for extra creaminess. If using full-fat coconut milk, you’ll want to add a splash of fresh lime juice to balance out the richness of the sauce.
Chicken – Shredded chicken is my go-to for this recipe, but baked, grilled, or rotisserie chicken are all great options. Whatever you use, make sure it’s very lightly seasoned so as not to clash with the flavors in the skillet.

Ingredient Swap: Swap the chicken for cooked steak or shrimp. Or, use cooked beans for a vegetarian option.

Cheese- I like using shredded sharp cheddar, but a Mexican blend or pepper jack also works great. For a dairy-free option, look for a good melting cheese. I’ve had success with the Daiya Oat Milk Cheese blend—it melts beautifully in casseroles like this.
Tortilla Chips – Sprinkle gluten-free tortilla chips on top of the skillet for a satisfying crunch. If you’re looking for a corn-free tortilla chip, Sieta make delicious grain-free tortilla chips that work well in this dish.

How to Make a Single Skillet Chicken Fajita Casserole Recipe (in under an hour!)

Before you begin, preheat your oven to 375°F.

Sauté. Heat olive oil in a large skillet over medium heat, and soften the onion and pepper. Then, stir in the garlic, and cook just until fragrant. Be careful not to burn!
Cook. Stir in the diced sweet potatoes, cover, and cook until fork-tender, stirring once or twice. Add more oil as needed if the veggies begin to stick to the pan!

Freshly sautéed green bell peppers and onions in a black skillet with a wooden spoon.

seasoned Diced potatoes, green bell peppers, and onions sautéing in a black skillet with a wooden spoon.

Season. Stir in the seasonings, transfer the veggie mixture to a bowl, and set aside.
Whisk. In the same skillet, heat more oil (or butter if you don’t need your chicken fajita skillet to be dairy-free). Then, whisk in the milk or broth, and bring the liquid to a gentle simmer. Make sure to scrape up the browned bits from the bottom of the pan! They add so much flavor. Then, stir in the diced tomatoes.
Thicken. Whisk in the scratch slurry, using just a little bit at a time, until the sauce thickens and becomes creamy. Add lime juice, if needed.

Hand pouring milk from a measuring cup into a skillet to create sauce base.

Tomato-based sauce with spices simmering in a skillet, stirred with a wooden spoon.

Combine. Stir in the shredded chicken, half of the veggie mixture, and shredded cheese.
Layer. Spread the remaining veggies over the top of the meat mixture. Then, add the tortilla chips and more cheese.

Shredded chicken mixed into a tomato-based sauce in a skillet, stirred with a wooden spoon.

Casserole skillet layered with tortilla chips and shredded cheese before baking.

Bake. Transfer the skillet to the oven, and bake just until the cheese is melted and the filling is hot, bubbly, and golden around the edges.
Serve. Enjoy warm with all your favorite toppings such as sour cream or dairy-free yogurt, avocado or guacamole, extra cheese, and fresh cilantro.

Baked chicken fajita casserole in a skillet with a serving spoon, no toppings. Small side bowls of fresh tomato and cilantro sit nearby.

Chicken fajita casserole in a skillet after serving, showing melted cheese, tomato topping, and cilantro with a large spoon scooping out a portion.

Pro-Tip: For extra toasty edges, broil for one minute at the very end of cooking. Just be sure to keep a close eye on your oven so as not to let your fajita casserole burn!

Serving Suggestions

With protein, fats, carbs, and fiber, this chicken fajita casserole is plenty filling enough to enjoy on its own. However, you can never go wrong with a side of gluten-free tortilla chips, vegan salsa con queso, fresh salsa, and guacamole.

Make Ahead, Storage, and Reheating

Cover leftovers tightly, and refrigerate them for up to 3 days. The chips will soften, but the flavor will still be delicious.

To reheat, warm in the oven at 350°F until heated through for the best texture, or microwave in short bursts for a quick option. Add a few fresh tortilla chips on top or serve with extra tortilla chips for extra crunch.

You can also freeze leftover fajita chicken casserole. However, for the best texture, I recommend freezing the cooked chicken, sautéed veggies, and sauce in separate containers for up to 3 months. When ready to eat, thaw them in the fridge overnight. Then, assemble with fresh tortilla chips and cheese before baking.

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