Preheat oven to 350°F (175°C).

Bring a large pot of salted water to a boil. Cook jumbo shells 8–10 minutes until al dente. Drain and cool on a tray to prevent sticking.

Shred cheeses and chop the onion while shells cook.

Heat a large skillet over medium-high heat. Add the ground beef and chopped onion. Cook, breaking up the meat, until beef is browned and onions are translucent, about 6–8 minutes.

Drain excess grease if desired. Stir in salsa and simmer 2–3 minutes. Taste and adjust seasoning.

Spoon about 2–3 tablespoons of the beef mixture into each cooled shell. Place stuffed shells, seam-side up, in a lightly oiled 9x13-inch baking dish.

Mix the shredded cheddar and Monterey Jack together and sprinkle about two-thirds over the stuffed shells. Reserve the rest for topping.

Cover the dish with foil and bake at 350°F for 15–20 minutes to heat through.

Remove foil, add remaining cheese, and bake 5–8 more minutes until cheese is bubbly and slightly golden.

Let rest 5 minutes before serving. Garnish with salsa, sour cream, sliced green onions, or cilantro if desired.