
This butternut squash-stuffed shells recipe transforms ordinary pasta into a comforting, seasonal delight that balances creamy cheese with sweet squash. I discovered this combination when looking for ways to use up fall harvest vegetables, and it's become a staple in my dinner rotation.
I first created this dish for a potluck dinner party, and it disappeared faster than any other dish on the table. Now my family requests it regularly throughout fall and winter months.
Ingredients
- Jumbo pasta shells: look impressive and hold the perfect amount of filling
- Butternut squash: provides natural sweetness and velvety texture
- Ricotta cheese: creates a creamy, smooth base for the filling
- Mozzarella cheese: delivers that irresistible melty stretch
- Parmesan: adds a sharp, salty bite that balances the sweet squash
- Garlic and onion powder: provide aromatic depth without the work of fresh aromatics
- Marinara sauce: brings acidity that cuts through the richness
- Fresh basil: brightens everything with a pop of color and freshness
Step-by-Step Instructions
- Pasta Preparation:
- Cook jumbo shells until they're just al dente, about 8 minutes. They'll continue cooking in the oven, so slightly undercook them to prevent mushiness. After draining, lay them out separately on a baking sheet to prevent sticking.
- Squash Cooking:
- Steam or boil butternut squash cubes until they're fork tender, approximately 10 to 15 minutes. Drain thoroughly and mash while still warm for the smoothest texture. Let it cool slightly before combining with cheeses to prevent the cheeses from melting prematurely.
- Filling Creation:
- Combine the mashed butternut squash with ricotta, half the mozzarella, Parmesan, and seasonings until everything is completely incorporated. Taste and adjust seasoning before stuffing the shells. The filling should be thick enough to hold its shape but soft enough to work with.
- Assembly Process:
- Spread half the marinara sauce evenly across your baking dish. Using a spoon or piping bag, generously fill each shell with about 2 tablespoons of filling. Arrange stuffed shells in the baking dish with slight space between them to allow even heating.
- Baking Perfection:
- Cover the filled shells with remaining sauce and sprinkle with reserved mozzarella. Bake uncovered until the cheese becomes golden and bubbly, and the edges of the shells turn slightly crispy, about 25 to 30 minutes.

Butternut squash is truly the star ingredient here. I love how its natural sweetness develops during roasting, creating a complexity that store bought alternatives just can't match. My youngest daughter, who normally avoids vegetables, devours these shells without hesitation.
Storage Tips
These stuffed shells maintain their quality remarkably well in the refrigerator. Store leftovers in an airtight container for up to 4 days. For best results when reheating, add a splash of water or extra marinara sauce before covering with foil and heating at 350°F until warmed through, about 15 minutes.
Make It Your Own
While this recipe is delicious as written, it welcomes customization. Try adding sautéed spinach, kale, or chard to the filling for extra nutrition and color. For meat lovers, incorporate cooked Italian sausage or pancetta. If you prefer a nuttier flavor profile, add a handful of toasted pine nuts or walnuts to the filling mixture.
Serving Suggestions
These stuffed shells pair beautifully with a simple arugula salad dressed with lemon vinaigrette to cut through the richness. For a complete meal, serve alongside garlic bread or rosemary focaccia to soak up the extra sauce. A glass of light bodied red wine like Chianti or Pinot Noir complements the flavors perfectly.
Recipe FAQs
- → Can I prepare these stuffed shells ahead of time?
Yes! You can assemble the entire dish up to 24 hours in advance and store it covered in the refrigerator. When ready to serve, simply bake for an additional 5-10 minutes since the shells will be cold from refrigeration.
- → What can I substitute for butternut squash?
Sweet potato, pumpkin, or acorn squash work well as substitutes with similar cooking times and flavor profiles. Each will bring its unique taste while maintaining the creamy texture needed for the filling.
- → How do I make this dish vegan?
Substitute the ricotta with cashew or tofu-based ricotta alternative, and use plant-based mozzarella and parmesan alternatives. The rest of the ingredients are naturally vegan-friendly.
- → What sides pair well with stuffed shells?
A simple green salad with vinaigrette dressing, garlic bread, roasted vegetables, or sautéed spinach all complement the rich flavors of the stuffed shells beautifully.
- → Can I freeze these stuffed shells?
Yes, these freeze exceptionally well. Assemble the dish but don't bake it. Cover tightly with foil and freeze for up to 3 months. When ready to serve, bake from frozen at 375°F for about 45-50 minutes until heated through and bubbly.
- → How do I know when butternut squash is properly cooked?
Butternut squash is properly cooked when it can be easily pierced with a fork and mashes without resistance. Undercooked squash will be firm and difficult to mash, while overcooked squash may become too watery.