Preheat and prep. Heat your oven to 400°F (200°C).
Lightly grease a 9x13-inch baking dish.
Slice the chicken and veggies. Cut chicken into thin strips, about 1/2 inch wide. Slice peppers and onion into similar-sized strips so they cook evenly.
Season. In a large bowl, toss chicken, peppers, and onion with olive oil, fajita seasoning, smoked paprika, chili flakes (if using), and a pinch of salt and pepper. Make sure everything is well coated.
Make the creamy protein base. In a separate bowl, whisk Greek yogurt, cream cheese, half the shredded cheese, lime juice, garlic, and a pinch of salt.
The mixture should be smooth and spreadable.
Assemble the casserole. Spread half the seasoned chicken and veggies in the baking dish. Dollop and spread half the yogurt mixture over the top. Repeat with the remaining chicken/veggies and the rest of the yogurt mixture.
If using black beans or corn, scatter them evenly between the layers.
Bake covered, then uncovered. Cover loosely with foil and bake for 15 minutes. Remove the foil, sprinkle on the remaining cheese, and bake another 10–15 minutes until the chicken is cooked through (165°F/74°C) and the top is lightly golden.
Rest and garnish. Let it rest for 5–10 minutes so the juices settle. Top with chopped cilantro and an extra squeeze of lime.
Serve your way. Spoon into bowls, over cauliflower rice or brown rice, or tuck into warm tortillas.
Add salsa or hot sauce if you like more heat.