In a large skillet over medium heat, add ground beef and diced onion. Cook, breaking up the meat, until browned and the onion is soft and translucent, about 6–8 minutes. Drain excess grease if needed.

Add garlic and cook for 30 seconds, just until fragrant.

Stir in taco seasoning, green chiles, and tomato sauce. Cook for 1–2 minutes, allowing the tomato sauce to reduce and coat the beef.

Pour in water and stir well. Simmer for 2–3 minutes until slightly thickened.

Reduce heat to low and add cream cheese. Stir until fully melted and smooth. Remove from heat and stir in ¼ cup reserved pasta water to keep the filling creamy.

Preheat oven to 350°F.

In a bowl, mix salsa and ½ cup of the taco sauce. Spread evenly across the bottom of a 9×13 baking dish.

Spoon taco beef mixture into each pasta shell and arrange shells open-side up in the baking dish.

Drizzle remaining ¼ cup taco sauce evenly over the stuffed shells.

Sprinkle cheddar and Monterey Jack (or Pepper Jack) cheese evenly over the top.

Cover loosely with foil and bake for 15 minutes. Uncover and bake an additional 5–10 minutes, until heated through and the cheese is melted and bubbly.

Let rest for 5 minutes before serving. Add desired toppings and serve warm.