Bring a large pot of salted water to a boil and cook the jumbo pasta shells according to package directions until just al dente. Drain and set aside to cool slightly.
In a large skillet over medium heat, cook the Italian sausage with the diced onion until the sausage is browned and the onion is soft. Add the minced garlic and cook for one more minute.
Stir the chopped spinach into the skillet and cook until wilted. Remove the skillet from heat and let the mixture cool for a few minutes.
In a mixing bowl, combine the ricotta cheese, 1 cup of mozzarella, Parmesan cheese, Italian seasoning, salt, and pepper. Add the cooled sausage and spinach mixture and stir until evenly mixed.
Spread 1 cup of marinara sauce in the bottom of a baking dish. Spoon the filling into each cooked shell and arrange them in the dish. Pour the remaining marinara sauce over the top and sprinkle with the remaining 1/2 cup of mozzarella.
Bake at 375°F for 20 to 25 minutes until the cheese is melted and bubbly. Let the shells rest for 5 minutes before serving.