Cook the Pasta Shells : Bring a large pot of salted water to a boil. Cook pasta shells according to package instructions until al dente. Drain and lay shells flat on a baking sheet to prevent sticking.
Prepare the Marinara Sauce: Heat olive oil in a skillet over medium heat. Add chopped onion and sauté until soft, about 3–4 minutes. Add garlic, cook for 30 seconds until fragrant. Stir in marinara sauce, dried basil, oregano, salt, and pepper. Simmer for 5–10 minutes.
Make the Spinach u0026 Ricotta Filling: In a large bowl, combine ricotta cheese, 1 cup mozzarella, Parmesan, chopped spinach, minced garlic, egg, salt, pepper, and nutmeg (if using). Mix until smooth and well combined.
Stuff the Shells: Spoon about 2 tbsp of filling into each cooked shell. Place filled shells seam side up in a greased baking dish.
Assemble the Dish: Spread a thin layer of marinara sauce on the bottom of the baking dish. arrange stuffed shells over the sauce. Pour remaining marinara sauce evenly over the shells. Sprinkle extra mozzarella and Parmesan cheese on top.
Bake: Preheat oven to 375°F (190°C). Cover the dish with foil and bake for 25 minutes. Remove foil and bake an additional 10 minutes until cheese is melted and bubbly.