Start by washing and chopping your vegetables. Dice the red bell pepper, zucchini, yellow squash, and onion into bite-sized pieces. Mince the garlic and jalapeño. Set the vegetables aside.
In a large skillet, heat the olive oil over medium heat. Add the chopped onion and cook until translucent, about 3-4 minutes. Then, add the red bell pepper, zucchini, and yellow squash. Season with kosher salt and black pepper to taste. Sauté until the vegetables are tender, around 5-7 minutes.
Stir in the minced garlic and jalapeño, cooking for another minute until fragrant. Add the black beans, green chiles, cumin, chili powder, and paprika. Mix until everything is well combined and heated through. Remove from heat and fold in the chopped cilantro.
Preheat your oven to 350°F (175°C). In your baking dish, spread a thin layer of enchilada sauce on the bottom. Take a corn tortilla and spoon a generous amount of the vegetable mixture in the center. Top with a sprinkle of cheese. Fold the tortilla over and place it seam-side down in the dish. Repeat with the remaining tortillas, stacking them in the dish.
Once all the tortillas are stacked, pour the remaining enchilada sauce over the top, ensuring they are well covered. Sprinkle the remaining cheese over the sauce.
Cover the baking dish with aluminum foil and place it in the preheated oven. Bake for about 20 minutes. Remove the foil and continue baking for an additional 10-15 minutes, or until the cheese is bubbly and golden.
Remove from the oven and let the enchiladas cool for a few minutes. Top with your choice of optional toppings like fresh cilantro, sliced jalapeños, avocado, green onions, or a dollop of sour cream. Slice and serve warm, and enjoy the vibrant flavors of your Stacked Vegetable Enchiladas!