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Baked butternut squash stuffed shells in a white baking dish next to a striped towel
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5 from 8 votes

Butternut Squash Stuffed Shells

These butternut squash stuffed shells have the perfect fall flavors of sage and butternut mixed with a creamy cheese sauce. This vegetarian dish is cozy and comforting, plus a great way to sneak in some extra vegetables!
Prep Time20 mins
Cook Time25 mins
Total Time45 mins
Course: Dinner
Cuisine: American
Servings: 4 people
Calories: 683kcal
Author: Alicia


  • 12 oz jumbo pasta shells
  • 15 oz can of butternut squash*
  • 1.5 cups ricotta cheese
  • 2 tablespoons fresh sage leaves, minced
  • 1 cup fresh kale or spinach, chopped
  • 1 teaspoon kosher salt
  • ¼ teaspoon black pepper
  • pinch of nutmeg

Creamy Bechamel Sauce

  • 2 tablespoons butter
  • 2 tablespoons all purpose flour
  • ¾ cup milk
  • ¾ cup vegetable broth
  • 3 ounces chèvre goat cheese


  • Preheat oven to 350 degrees F. Cook the pasta according to package directions for "al dente", usually on the lower end of the cooking time. The pasta should be softened, but still firm (not mushy). Drain and set shells aside on a towel. Grease a 9x13 inch pan with a little olive oil or extra butter. In a large bowl, combine the butternut squash with ricotta, sage, chopped kale or spinach, salt, pepper, and a pinch of nutmeg. Taste and adjust any seasonings. Fill each pasta shell with the butternut/ricotta mixture and set inside the 9x13 inch pan.
    Unbaked butternut squash stuffed shells in a white baking dish
  • In a large saucepan, melt the butter over medium-low heat. Stir in the flour till smooth and cook until lightly browned and bubbly. Add the milk and broth in parts, whisking after each addition until smooth. Initially it will be clumpy, but don't worry, just keep whisking till it smooths out - this is why it's helpful to do in smaller parts. Bring the sauce to a simmer (small bubbles), stirring until thickened, about 6-8 minutes. Turn off the heat and stir in goat cheese until smooth. Add any salt and pepper as needed.
  • Pour the sauce over and around the shells. Bake at 350 degrees F for 25 minutes until lightly browned and bubbly on the top. Serve warm!


  • The serving size calculated for this is for 4 people, which is a very generous serving that would be a full meal. This could stretch to serve 6 people easily. For those with Meniere's please use the sodium count as a guideline and understand it is much higher with the program I use than if making your own broth/adjusting sodium.
  • For migraine-friendly, check the ricotta cheese for additives (use brands suggested in post) and also use homemade vegetable broth from my cookbook or this chicken stock. You can find more information on stock/broth here
  • I find canned butternut squash the fastest/easiest, but see the post for suggestions for cooking fresh in an instant pot. 
  • I have not tried to make this dairy free, but if you wanted to, you could try leaving out the ricotta and using more butternut squash, substituting the butter for ghee or oil, and using oat milk for the sauce.
  • I have also not seen these large shells sold gluten free, but if you can find them it's a very easy substitute. Use your favorite gluten free AP flour or arrowroot to thicken the sauce.  


Calories: 683kcal | Carbohydrates: 86g | Protein: 29g | Fat: 25g | Saturated Fat: 15g | Cholesterol: 76mg | Sodium: 823mg | Potassium: 803mg | Fiber: 5g | Sugar: 8g | Vitamin A: 13853IU | Vitamin C: 42mg | Calcium: 366mg | Iron: 3mg