Preheat oven to 375 degrees F. Lightly spray a 9x13-inch baking dish with cooking spray.
Place the chicken breasts in the baking dish in a single layer. Sprinkle 1/2 tablespoon of fajita seasoning evenly over the chicken.
Arrange the sliced bell peppers and onion over and around the chicken. Sprinkle the remaining 1/2 tablespoon fajita seasoning over the vegetables.
Cover the baking dish tightly with foil and bake for 25–30 minutes, or until the chicken is nearly cooked through.
Remove the foil and sprinkle the Mexican cheese evenly over the chicken and vegetables.
Top with the crushed tortilla chips.
Return to the oven, uncovered, for 8–10 minutes, until the cheese is melted and the tortilla topping is golden and crispy. The chicken should reach 165°F in the thickest part.
Let the casserole rest for about 5 minutes before serving.