Three Cheese Butternut Squash Stuffed Shells

  • Author: Cassie Johnston
  • Prep Time: 20 mins
  • Cook Time: 40 mins
  • Total Time: 1 hour
  • Yield: 8 servings 1x


These Three Cheese Butternut Squash Stuffed Shells are the ultimate in Fall comfort food.



For the Sauce

  • 6 tablespoons butter
  • 5 tablespoons all purpose flour
  • 2 cups chicken or vegetable broth
  • 2 cups half and half
  • 2 teaspoons salt, plus more to taste
  • 1 teaspoon garlic powder
  • 1/4 teaspoon freshly ground nutmeg
  • 1/2 cup shredded parmesan cheese, plus additional for garnish

For the Shells

  • 16 ounces ricotta cheese
  • 1 1/2 cups butternut squash puree
  • 2 cups shredded mozzarella cheese, divided
  • 2 eggs
  • 1/2 teaspoon salt
  • 1/2 teaspoon pepper
  • 1/4 cup chopped fresh sage, plus additional for garnish
  • 12 ounces jumbo shells, cooked al dente, drained and rinsed


  1. To make the sauce: Melt the butter over medium-high heat in a large saucepan. Whisk in the flour, and continue to cook until the mixture turns slightly golden brown—about 2-3 minutes.
  2. Slowly whisk in the broth until all lumps are dissolved. Then add in the half and half, salt, and garlic powder. Continue to heat over medium-high heat, stirring frequently, until the sauce is thick enough to coat the back of a spoon—about 15 minutes. Watch carefully for scorching, you don’t want the sauce to simmer or boil.
  3. Remove from heat and stir in the nutmeg and parmesan.
  4. Preheat oven to 350°. Spread about 1 cup of the sauce in the bottom of a large casserole dish (the biggest you have—at least a 13″ x 9″). Set aside.
  5. To make the filling: in a large mixing bowl, stir together the ricotta, squash puree, 1 cup of mozzarella, eggs, salt, pepper, and sage until smooth.
  6. Fill the cooked shells with the ricotta mixture (I used about 3 tablespoons per shell, but your shell size may vary). Place the shells, seam-side down, in the prepared baking dish. Repeat with the remaining shells and filling—really packing them into the baking dish.
  7. Pour remaining sauce over the shells, and then sprinkle with the remaining mozzarella. Bake in preheated oven for 30-40 minutes, or until bubbly and browned on top. Serve topped with additional fresh sage and parmesan.


Bet you didn’t know you can get frozen butternut squash! Most supermarkets will carry it in at least one form—either puree or cooked cubes you can mash for this recipe. Check in the frozen veggie aisle. It’s a great time saver! You can also use canned pumpkin puree.

Make sure you rinse your shells using cool water after draining. Why? It helps cool the pasta down so you can handle them, but also removes much of the starch that makes the shells stick together—making them hard to separate to fill.

Best way to fill stuffed shells—grab a large zip-top bag, fill with the filling, and the clip off the corner. Pipe the filling to the shells using the makeshift piping bag.

This recipe easily will serve 8. It’s a great freezer dish if you need to serve fewer than that. Just divide the shells between two square baking dishes—freeze one and cook the other.