In a large skillet over medium-high heat, brown the ground beef until fully cooked. Drain any excess fat. Add the refried beans, chopped onion, minced garlic, ½ cup of the tomato sauce, chili powder, cumin, oregano, salt, and pepper. Stir the mixture thoroughly and cook for an additional 5 minutes, allowing the flavors to meld and the onion to soften slightly.

Place the flour tortillas on a microwave-safe plate and warm them in the microwave for 30–40 seconds. This will make them more pliable and easier to roll without tearing.

Divide the beef mixture evenly among the tortillas, placing the filling in the center of each. Fold one end of the tortilla over the filling, tuck in the sides, and continue to roll it tightly to form a sealed packet. Secure the seam side with a toothpick if needed.

Pour approximately 1 inch of oil into a deep-sided skillet. Heat the oil over medium-high heat. Carefully place the rolled chimichangas seam-side down into the hot oil. Fry each chimichanga until it is golden brown and crispy on all sides, turning as needed. Once cooked, transfer to a paper towel-lined tray to drain excess oil.

In a separate saucepan, combine the remaining tomato sauce, diced green chiles, and chopped jalapeños. Heat the mixture over medium heat until warmed through. Season with additional salt and pepper to taste if desired.

Place the cooked chimichangas on serving plates. Ladle the warmed sauce over the top of each chimichanga, then sprinkle generously with shredded cheese. Serve immediately while hot.