Preheat your oven to 375°F (190°C) and lightly grease a 9×13 inch baking dish.
Cook the pasta shells according to package instructions, but keep them slightly underdone (about 1-2 minutes less than directed). They’ll continue cooking in the oven. Drain and set aside on a baking sheet to cool.
Prepare the filling by combining ricotta cheese, 1 cup mozzarella, 1/2 cup Parmesan, eggs, drained spinach, chopped herbs, garlic, salt, pepper, and nutmeg in a large mixing bowl. Mix thoroughly until well combined.
Spread 1 cup of marinara sauce evenly across the bottom of your prepared baking dish.
Fill each pasta shell with a generous spoonful of the ricotta mixture (about 1.5-2 tablespoons each) and arrange them in a single layer in the baking dish.
Pour the remaining marinara sauce over the filled shells, making sure to cover them evenly. The sauce protects the pasta from drying out during baking.
Sprinkle the remaining mozzarella and Parmesan cheese over the top of the shells.
Cover the baking dish with foil and bake for 25 minutes. Then remove the foil and bake for an additional 5-10 minutes until the cheese is bubbly and slightly golden.
Let the dish rest for 5 minutes before serving. Garnish with fresh basil leaves and offer red pepper flakes on the side for those who enjoy a touch of heat.