If you’re craving a cozy, comforting dish that sings with fall flavors, the Butternut Squash and Cheese Stuffed Pasta Shells Recipe is going to become your new favorite. Creamy butternut squash blends beautifully with a trio of cheeses, nestled inside perfectly cooked jumbo pasta shells, all baked with a luscious marinara sauce. This dish is a wonderful way to enjoy a rich, satisfying meal that feels both homely and a little special. Whether you’re cooking for family or friends, it’s sure to be a crowd-pleaser!

Ingredients You’ll Need
Everything you need for this recipe is wonderfully simple yet essential for achieving that perfect balance of creamy, savory, and subtly sweet flavors. Each ingredient plays a key role in building texture, richness, and vibrant color that makes the dish as delightful to look at as it is to eat.
- 12 ounces jumbo pasta shells: These act like little cozy boats, holding the delicious filling perfectly.
- 2 cups butternut squash, peeled and cubed: The star ingredient that brings natural sweetness and creamy texture when mashed.
- 1 tablespoon olive oil: Helps roast the squash to tender perfection with a slight caramelized flavor.
- 1/2 teaspoon salt: Enhances overall flavor and seasons the squash just right.
- 1/4 teaspoon black pepper: Adds a subtle spicy note to balance the dish.
- 1 cup ricotta cheese: Provides a soft, creamy base for the filling.
- 1 cup shredded mozzarella cheese: Melts beautifully to give gooey, cheesy goodness inside and on top.
- 1/2 cup grated Parmesan cheese: Adds a punch of savory, nutty flavor that deepens the profile.
- 2 cloves garlic, minced: Infuses a fragrant, savory warmth.
- 1/2 teaspoon dried sage: A perfect herb match for butternut squash, adding earthy, slightly peppery notes.
- 1/2 teaspoon dried thyme: Brings a fresh, subtle herbaceous layer.
- 2 cups marinara sauce: The rich, tangy sauce that coats and complements the stuffed shells beautifully.
- 1/4 cup fresh basil, chopped (optional, for garnish): Adds a bright, fresh pop of color and flavor when serving.
How to Make Butternut Squash and Cheese Stuffed Pasta Shells Recipe
Step 1: Prepare Your Oven and Pasta Shells
Start by preheating your oven to 375°F (190°C). Meanwhile, cook your jumbo pasta shells according to the package instructions until al dente. This ensures they will hold their shape during baking without becoming mushy. Drain them and set them in a single layer on a tray to avoid sticking. This simple prep step lays the foundation for perfectly textured pasta in your final dish.
Step 2: Roast the Butternut Squash
On a baking sheet, toss the peeled and cubed butternut squash with olive oil, salt, and pepper. Spread them out evenly so each piece roasts instead of steams. Roast in your preheated oven for about 25 to 30 minutes until tender and lightly caramelized. This roasting brings out the squash’s natural sweetness, making it the perfect base for your filling.
Step 3: Mash and Flavor the Squash Filling
Once the roasted squash has cooled just enough to handle, mash it in a bowl until smooth. Then combine the mashed squash with ricotta, half of the mozzarella and Parmesan cheeses, minced garlic, dried sage, and thyme. Mixing these ingredients thoroughly blends creamy textures and earthy herbs with that sweet, smooth squash, crafting a filling that’s both flavorful and satisfying.
Step 4: Stuff the Pasta Shells
Take your cooked pasta shells and carefully spoon the squash and cheese mixture into each one. It’s a satisfying step watching those shells transform into little bundles of deliciousness. Arrange the stuffed shells side by side in a single layer within your baking dish, ensuring even baking later on.
Step 5: Layer with Sauce and Cheese
Pour the marinara sauce evenly over the arranged shells, allowing it to fill the gaps and coat each shell gently. Then sprinkle the remaining mozzarella and Parmesan cheeses over the top. This cheesy topping melts into a golden, bubbly finish once baked and adds the perfect balance between rich filling and tangy tomato flavors.
Step 6: Bake to Perfection
Cover your baking dish with foil to keep everything moist and bake in the preheated oven for 25 minutes. After that, remove the foil and bake for another 10 minutes, or until the cheese is melted, golden, and bubbly. This last step gives you that irresistible texture contrast — melty cheese on top with a warm, tender filling inside.
How to Serve Butternut Squash and Cheese Stuffed Pasta Shells Recipe

Garnishes
Fresh basil chopped and sprinkled on top just before serving adds a lovely burst of green color and a fragrant lift to the dish. It’s a small touch that makes a big impression on both the eyes and the taste buds, enhancing the wholesome flavors.
Side Dishes
This dish pairs beautifully with a crisp green salad with vinaigrette to cut through the richness or some garlic bread to scoop up any remaining sauce. Lightly steamed green vegetables like asparagus or sautéed spinach also complement the stuffed shells without overpowering them.
Creative Ways to Present
For an elegant dinner party, plate a few stuffed shells on a large white plate, drizzle with extra marinara sauce, and garnish with basil and freshly grated Parmesan. Alternatively, for family-style meals, bring the whole baking dish to the table, letting guests serve themselves and enjoy the rustic, comforting charm of this recipe.
Make Ahead and Storage
Storing Leftovers
Leftover stuffed shells can be tightly covered with plastic wrap or foil and stored in the refrigerator for up to 3 to 4 days. This dish actually tastes fantastic the next day as the flavors deepen and meld together overnight.
Freezing
You can freeze the cooked butternut squash and cheese stuffed pasta shells recipe either before or after baking. Arrange them in an airtight container or freezer-safe dish, separating layers with parchment paper, and freeze for up to 2 months. Thaw in the fridge overnight before reheating for best results.
Reheating
To reheat, cover the dish with foil and warm in a 350°F (175°C) oven for about 20-25 minutes until heated through. Alternatively, microwave individual portions covered loosely with a damp paper towel for 2 to 3 minutes. The cheese will delightfully melt again, and the flavors come alive just like freshly baked.
FAQs
Can I use a different type of squash?
Absolutely! Butternut squash is preferred for its sweetness and creamy texture, but acorn or kabocha squash can work as substitutes if you roast them until fork-tender first. The flavor will vary slightly but remain delicious.
Is there a vegetarian version of this recipe?
This recipe is naturally vegetarian since it uses no meat but relies on cheeses and veggie ingredients. Just be sure your marinara sauce doesn’t contain meat stock or added meat pieces.
Can I make this gluten-free?
Yes! Just swap the jumbo pasta shells for gluten-free pasta shells or a similar gluten-free pasta shape, and prepare the recipe as usual for a gluten-friendly option that doesn’t compromise on flavor.
How can I make this dish vegan?
To go vegan, substitute the ricotta, mozzarella, and Parmesan cheeses with plant-based alternatives—many brands offer dairy-free ricotta and mozzarella now. Ensure the marinara sauce is vegan as well. Roasting the butternut squash with oil, herbs, and seasoning stays the same.
Can I prepare the filling in advance?
Yes! You can prepare the squash and cheese filling a day ahead and refrigerate it. When ready to assemble, cook the shells, stuff them, and bake as directed. This makes hosting or weeknight dinners easier and more stress-free.
Final Thoughts
This Butternut Squash and Cheese Stuffed Pasta Shells Recipe is a true celebration of cozy, comforting flavors wrapped up in a beautiful, cheesy package. It’s a fantastic way to bring seasonal produce into your kitchen with a recipe that feels both homey and special enough to share. Once you try it, you’ll find yourself making it again and again for friends, family, or whenever you need a little extra delicious warmth on your plate.
Print
Butternut Squash and Cheese Stuffed Pasta Shells Recipe
- Prep Time: 0h 20m
- Cook Time: 1h 0m
- Total Time: 1h 20m
- Yield: 4-6 servings
- Category: Main Course
- Method: Baking
- Cuisine: Italian
- Diet: Vegetarian
Description
These Butternut Squash and Cheese Stuffed Pasta Shells offer a comforting and flavorful vegetarian dish featuring tender roasted butternut squash blended with creamy ricotta and melted cheeses, all baked in jumbo pasta shells and smothered in marinara sauce. Perfect as a hearty main course for fall or any time you crave a cheesy, autumn-inspired meal.
Ingredients
Pasta
- 12 ounces jumbo pasta shells
Butternut Squash and Seasoning
- 2 cups butternut squash, peeled and cubed
- 1 tablespoon olive oil
- 1/2 teaspoon salt
- 1/4 teaspoon black pepper
Cheese Filling
- 1 cup ricotta cheese
- 1 cup shredded mozzarella cheese (divided)
- 1/2 cup grated Parmesan cheese (divided)
- 2 cloves garlic, minced
- 1/2 teaspoon dried sage
- 1/2 teaspoon dried thyme
Sauce and Garnish
- 2 cups marinara sauce
- 1/4 cup fresh basil, chopped (optional, for garnish)
Instructions
- Preheat the oven: Preheat your oven to 375°F (190°C) to prepare for roasting the butternut squash and baking the stuffed shells.
- Cook pasta shells: Boil the jumbo pasta shells according to the package directions until al dente. Drain and lay them out in a single layer to prevent sticking while you prepare the filling.
- Roast butternut squash: Toss the peeled and cubed butternut squash with olive oil, salt, and pepper on a baking sheet. Spread evenly and roast in the oven for 25-30 minutes until tender and slightly caramelized.
- Mash the squash: Remove the roasted squash and allow it to cool slightly. Transfer to a bowl and mash until smooth and creamy, which will be the base for the filling.
- Prepare filling: Combine the mashed butternut squash with ricotta, half of the mozzarella (1/2 cup), half of the Parmesan (1/4 cup), minced garlic, dried sage, and dried thyme. Mix thoroughly to create a flavorful and creamy mixture.
- Stuff shells: Spoon the cheese and squash filling into each cooked pasta shell. Arrange the stuffed shells in a single layer inside a baking dish to ensure even cooking.
- Add marinara sauce: Pour the marinara sauce evenly over the stuffed shells, coating them well for moisture and flavor.
- Add remaining cheese: Sprinkle the leftover mozzarella (1/2 cup) and Parmesan cheese (1/4 cup) over the top to create a cheesy crust once baked.
- Bake covered: Cover the baking dish with foil and bake in the preheated oven for 25 minutes. This helps heat everything through and meld the flavors.
- Bake uncovered: Remove the foil and bake for an additional 10 minutes until the cheese on top is melted, golden, and bubbly.
- Garnish and serve: Remove from oven and garnish with chopped fresh basil if desired. Serve the stuffed shells hot as a satisfying main dish.
Notes
- You can substitute fresh herbs for the dried sage and thyme for a brighter flavor.
- For a vegan version, use plant-based ricotta and mozzarella alternatives and adjust accordingly.
- Make sure to lay out cooked pasta shells in a single layer to avoid them sticking together while assembling.
- The roasted butternut squash can be prepared a day ahead to save time.
- Leftovers keep well refrigerated for 3 days and reheat nicely in the oven or microwave.

