While you prepare ingredients, bring a large pot of salted water to a boil. Finely dice the onion and mince the garlic cloves, then roughly chop the fresh spinach. Measure out the ricotta, cream cheese (ensuring it's softened), parmesan, mozzarella, and marinara sauce into separate bowls. Once water is boiling, add the jumbo pasta shells and cook until just al dente (about 1-2 minutes under the package time), then drain in a colander and spread them on a clean kitchen towel to cool and prevent sticking.

In a large mixing bowl, combine the softened cream cheese, ricotta cheese, and grated parmesan cheese, stirring until smooth and well blended. Add the shredded chicken, chopped spinach, minced garlic, diced onion, lightly beaten egg, fresh parsley, Italian seasoning, salt, black pepper, and red pepper flakes. Fold everything together gently but thoroughly, ensuring the ingredients are evenly distributed—I like to use a rubber spatula for this as it helps maintain the texture of the spinach and prevents overworking the mixture.

Preheat your oven to 350°F and lightly grease a 9x13 inch baking dish (or similar size). Spread about half of the marinara sauce evenly across the bottom of the prepared dish—this prevents the shells from sticking and creates a flavorful base layer.

Using a small spoon or piping bag, carefully fill each cooked shell with approximately 2-3 tablespoons of the filling mixture from Step 2, working gently to avoid tearing the pasta. Arrange the filled shells in the prepared baking dish in a single layer, nestling them close together but not overlapping. I find that arranging them seam-side down helps keep the filling inside and creates a more attractive presentation.

Pour the remaining marinara sauce evenly over the filled shells, making sure all are covered. Cover the baking dish tightly with aluminum foil, then place it in the preheated 350°F oven and bake for 40 minutes.

Carefully remove the foil from the baking dish and sprinkle the 1 1/4 cups of shredded mozzarella cheese evenly over the top of the shells. Return the uncovered dish to the oven and bake for an additional 5-10 minutes until the cheese is melted and lightly golden. Let the dish rest for 5 minutes before serving—this allows the cheese to set slightly and makes the shells easier to serve without falling apart.