Preheat oven to 350°F (175°C). Lightly oil a 9×13-inch baking dish.

Bring a large pot of salted water to a boil. Add jumbo shells and cook for 8-10 minutes until al dente. Drain and spread shells on a tray to cool.

In a skillet over medium-high heat, add ground beef and chopped onion. Cook until no pink remains and onions are soft, about 8-10 minutes. Drain excess fat if necessary.

Reduce heat to medium, stir in salsa, and cook for 1-2 minutes until combined. Remove from heat.

Stir in shredded cheddar and Monterey Jack cheese into the beef mixture until slightly melted. Season with salt and pepper to taste.

Fill each cooled shell with about 2-3 tablespoons of the beef-and-cheese mix and place them seam-side up in the prepared baking dish.

Sprinkle the remaining cheese evenly over the shells.

Cover with foil and bake for 15 minutes. Remove foil and bake an additional 5-7 minutes until cheese is bubbly and edges start to brown.

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