Heat oven to 375°F and lightly oil a 9x13-inch baking dish.
Bring a large pot of salted water to a boil.
Cook shells until just shy of al dente, 8–9 minutes. Drain and rinse cool.
Toss shells with olive oil to prevent sticking; set aside.
Mix pumpkin, ricotta, spinach, mozzarella, Parmesan, garlic, milk, sage, nutmeg, salt, and pepper until creamy.
Spread 1 cup marinara in the bottom of the prepared dish.
Fill each shell with a heaping spoonful of filling. Nestle seam up in the sauce.
Spoon remaining marinara over shells. Sprinkle remaining mozzarella and Parmesan on top.
Cover with foil and bake 20 minutes. Uncover and bake 10–15 minutes more until bubbly.
Rest 5 minutes before serving.