Preheat oven to 450°F.
Add the olive oil to a large oven-proof skillet over medium-high heat. Once shimmering, add the spinach and 2 tablespoons water. Cook stirring frequently until the spinach is wilted. Add the chicken, cumin, salt and pepper. Stir gently until combined and heated through. Transfer the mixture to a large bowl. Set aside.
In a medium bowl whisk together the enchilada sauce, sour cream and the minced chipotle peppers. Spoon about ¾ cup of the sauce into the bottom of the now empty skillet. Layer 4 tortillas over the sauce, overlapping the edges to cover the bottom of the skillet.
Top the tortillas with half the chicken and spinach mixture. Sprinkle with ⅓ of the onions and ⅓ of the cheese.
Spoon half the remaining sauce over the casserole, then repeat with 4 more tortillas, the remaining chicken mixture, half the remaining onion and half the remaining cheese.
Top with the last 4 tortillas, all the remaining sauce, then the onions and cheese.
Bake the casserole until hot and bubbling, about 10-15 minutes. Sprinkle with red onion, jalapeños and other desired toppings before serving.