Preheat oven to 350°F (175°C). Grease a 9x13-inch casserole dish and set aside.
Boil water and cook pasta shells according to package directions. Drain and set aside. You can spray with olive oil to prevent them from sticking together.
Heat a large skillet over medium heat. Add the ground beef, cooking until browned and no longer pink. Drain to remove excess grease from the skillet.
Add the taco seasoning mix and salsa to skillet. Stir and cook for an additional 2-3 minutes, until heated through and combined.
Remove skillet from heat and stir in ½ cup of each kind of shredded cheese. Stir in the diced green chilies.
Scoop the beef mixture into the cooked pasta shells, generously filling each shell. Place the filled shells in the greased baking dish.
Sprinkle the remaining shredded cheese evenly over the shells.
Cover the baking pan with aluminum foil and bake in preheated oven for 25-30 minutes, or until the cheese has melted and is bubbly.
Remove the foil from the pan and bake for an additional 5 minutes, or until the cheese has browned slightly.
Garnish with your choice of toppings, such as chopped tomatoes, diced avocado, sour cream, or chopped cilantro.