These Butternut Squash Stuffed Shells are creamy, cozy and full of fall flavor. Tender jumbo pasta shells are filled with roasted butternut squash, sweetened with a touch of maple syrup and baked in a parmesan sage sauce.
This is the perfect dish for a chilly night, a holiday dinner or even a small dinner party. A creamy sage sauce with subtle spice makes these stuffed shells the perfect way to enjoy the flavors of fall.
For more comforting fall meals, try our Spinach Lasagna Roll Ups and our Zuppa Toscana.
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Why You Will Love This Recipe
- Seasonal Comfort: Roasted butternut squash brings natural sweetness and creaminess that feels like fall.
- Crowd-Pleasing Flavors: Maple, sage, parmesan and nutmeg balances a sweet and savory profile.
- Perfect for Gatherings: Elegant enough for entertaining but simple enough for weeknights.
- Make-Ahead Friendly: You can prep the shells and sauce ahead of time, then bake before serving.
- Naturally Vegetarian: A hearty main that’s satisfying without meat.
Ingredients
This recipe uses simple ingredients that combine into a rich, creamy base with layers of flavor.
See the recipe card below for the exact quantities of each ingredient.
- Butternut Squash: Roasted until fork tender for natural sweetness and a creamy filling.
- Maple Syrup: Adds a touch of sweetness that pairs perfectly with squash.
- Nutmeg: Warm spice that enhances the cozy fall flavor.
- Unsalted Butter: Creates richness and depth in the creamy sauce.
- Fresh Sage: Brings an earthy, aromatic note to the sauce.
You'll want to have on hand a baking sheet, large pot, mixing bowl, small saucepan, measuring cups and spoons and 9x13 casserole dish.
Variations
- Ricotta Cheese Filling: Blend roasted squash with ricotta for a creamier filling and a classic taste.
- Tomato Sauce Base: Swap the white sauce for marinara sauce for a butternut squash lasagna–style twist.
- Cottage Cheese: Increase the protein with a scoop of cottage cheese to the filling.
- Red Pepper Flakes: Sprinkle in for a little heat that balances the sweetness of the squash.
- Brown Butter Sauce: Replace regular butter with brown butter for a nutty aroma and deeper flavor.
How to Make Butternut Squash Stuffed Shells
This stuffed shells recipe is easier than it looks, with minimal prep time and simple steps that come together into a cozy fall pasta dish.
Preheat oven to 400F and lightly spray a baking sheet with non-stick spray.
Place each half of the squash cut side down, then pour in enough water to fill ½ inch of the pan. Bake in preheated oven until very fork tender, about 30-45 minutes (depending on size). Remove when done and let cool enough to handle.
While the squash is roasting, cook pasta shells according to directions, until al dente, and set aside.
Remove the cooked squash with a spoon and place into a bowl, then discard the skins. Add in the maple syrup, nutmeg and sea salt and mix thoroughly.
For the sauce, melt butter in a saucepan over medium heat.
Pour in the heavy cream, sage and garlic salt. Reduce heat and continue to cook the sauce (without boiling), until it has slightly thickened, about 3-4 minutes.
Gradually add in the ½ cup of parmesan cheese and stir until completely melted.
Pour enough sauce to make a thin layer on the bottom of a baking dish.
Spoon about 2 tablespoons of butternut filling into each shell, and place in the dish. Repeat until all shells are filled, then pour remaining sauce over top. Sprinkle with remaining parmesan cheese.
Cover with foil if desired and bake until sauce starts to bubble (about 10-15 minutes).
Hint: Roast the squash well. Make sure it’s golden brown and caramelized for maximum flavor.
Recipe Tips
- Use Pasta Water: A splash can help thin the sauce without diluting the flavor, if needed.
- Cover with Foil: Ensures the shells keep from drying out before the cheese melts.
- Add Crispy Sage Leaves: Fry sage in a drizzle of olive oil for garnish and extra flavor.
- Mix Filling in a Food Processor: This creates a smoother texture for stuffing the shells.
Nothing says autumn quite like butternut squash! You may also want to try our Roasted Butternut Squash and Garlic Soup for the same delicious seasonal flavors.
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Storage Instructions
- Refrigerator: Store in an airtight container for 2-3 days.
- Freezer: This is a great recipe to meal prep and save for later. In an oven-safe dish, make the shells as you would but freeze before baking. Wrap in plastic wrap and aluminium foil then thaw in the fridge overnight, and allow them to come to room temperature before baking. They can last for up to 3 months this way.
- Reheating: When reheating or baking shells from room temperature, preheat oven to 400F and bake until the sauce bubbles and they are warmed throughout.
Serving Suggestions
- Simple Sides: Sautéed green beans with shallots or a roasted butternut squash soup.
- Complementary Mains: Herb butter turkey, roasted chicken, slow cooker brisket.
- Sweet Finish: Pumpkin banana bread, apple pie or pecan pie.
Recipe FAQs
No, you can roast the halves cut-side down, then scoop out the flesh once cooked. But if you want to roast them already cubed, you can and just bake until fork tender.
Yes, you can stuff the shells, assemble the dish and refrigerate covered with foil. Bake the next day for best results.
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Butternut Squash Stuffed Shells
Equipment
- Baking Sheet
- Large Pot
- Medium Saucepan
- Mixing Bowl
- Measuring Cups and Spoons
- 9x13 casserole dish
Ingredients
- 1 medium butternut squash enough to make 3 cups
- 18 large pasta shells 5.6 oz/ 160 grams
- 2 tablespoon pure maple syrup
- ¼ teaspoon ground nutmeg
- ¼ cup butter unsalted
- 1 ½ cups heavy cream
- 1 cup parmesan cheese grated and divided
- ¼ cup fresh sage packed and roughly chopped
- 2 teaspoon garlic salt
Instructions
- Preheat oven to 400F and lightly spray a baking sheet with non-stick spray.
- Place each half of the squash cut side down, then pour in enough water to fill ½ inch of the pan. Bake in preheated oven until very fork tender, about 30-45 minutes (depending on size). Remove when done and let cool enough to handle.
- While the squash is roasting, cook pasta shells according to directions, until al dente, and set aside.
- Remove the cooked squash with a spoon and place into a bowl, then discard the skins. Add in the maple syrup, nutmeg and sea salt and mix thoroughly.
- For the sauce, melt butter in a saucepan over medium heat.
- Pour in the heavy cream, sage and garlic salt. Reduce heat and continue to cook the sauce (without boiling), until it has slightly thickened, about 3-4 minutes.
- Gradually add in the ½ cup of parmesan cheese and stir until completely melted.
- Pour enough sauce to make a thin layer on the bottom of a baking dish.
- Spoon about 2 tablespoons of butternut filling into each shell, and place in the dish. Repeat until all shells are filled, then pour remaining sauce over top. Sprinkle with remaining parmesan cheese.
- Cover with foil if desired and bake until sauce starts to bubble (about 10-15 minutes).
Notes
- Roast the squash well. Make sure it’s golden brown and caramelized for maximum flavor.
- A splash of pasta water can help thin the sauce without diluting the flavor, if needed.
- Covering with foil isn’t required but it can ensure the shells do not dry out before the cheese melts.
- Fry sage leaves in a drizzle of olive oil for garnish and extra flavor.
- Make an extra smooth texture by running the filling through a food processor before stuffing the shells.
Nutrition
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Eva Filer says
This is one of my favorite recipes to make in the Fall. It is so much quicker than I think once you gather your ingredients and has so much flavor. It is a special request from one of my girlfriends for her birthday every year too!