Heat a large skillet over medium heat. Add the olive oil and onions and jalapeño. Cook for 5-7 minutes until softened. Transfer the onions and jalapeños to a plate. Set aside.
Add the ground beef to the skillet and cook for 8-10 minutes until the beef is cooked through, crumbling the meat as it cooks. Drain the excess fat.
Add the onions and jalapeño back to the skillet along with the green chiles. Stir to. Stir in 1½ cups of enchilada sauce. Simmer on low while prepping the tortillas.
Preheat a griddle pan over medium heat. Toast the flour tortillas on each side until lightly browned but still pliable.
Spread ¼ cup enchilada sauce in the bottom of the baking dish. Top each tortilla with some of the beef mixture and cheese. Roll up and place seam-side down in the prepared pan. Pour the remaining sauce over the tortillas. Top with the remaining cheese.
The enchilada sauce can be made up to several days in advance.
Toast the tortillas over a gas flame or on a griddle until they are lightly charred but still pliable. This helps to keep the tortillas from turning soggy in the casserole.
If assembling the enchiladas ahead of time, prep no more than 1 day in advance. Store the rolled tortillas separately from the sauce. Bring the dish to room temperature and cover the enchiladas with sauce and cheese before baking as indicated above.
Store leftovers in the refrigerator for 4-5 days. Reheat individual portions in the microwave. To reheat the casserole, cover, and heat in a 350-degree oven until warmed through.