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Butternut Squash and Cheese Stuffed Pasta Shells bake…best for nights when you’re craving Italian, but also craving those cozier fall flavors. Jumbo pasta shells stuffed with herb roasted butternut squash and ricotta cheese. Then baked in classic a marinara sauce that’s simple and so delicious. This is a great fall pasta to serve any night of the week – or for your next Saturday night dinner party!

This post is sponsored by Mezzetta®

Butternut Squash and Cheese Stuffed Pasta Shells |

It’s that time of year when our weather is really starting to turn cooler. The mornings and nights are cool and crisp, but the days are warm and sunny. It’s actually the most ideal weather you could ask for and has me so excited for the upcoming fall season.

I know many of you are still experiencing very hot days. But with fall just about one week away, the days will soon turn cooler for all of us. And when that happens, we’ve got your first fall pasta bake all ready to go.

I’m not ready for pumpkin just yet, but the autumn squash crops are harvesting. Which means acorn, spaghetti, and butternut squash are at their peak. I’m a fan of all fall squash. But butternut is almost always the first I roast up each season. And this year it’s in the form of these delicious pasta shells.

Butternut Squash and Cheese Stuffed Pasta Shells |

The quick details – the squash

What I love so much about this recipe is that while it looks fancy, it’s really pretty easy to create. Start with the squash, cut it into cubes, then toss it with fresh thyme and chili flakes.

Then take some prosciutto and drape it over the squash and throw everything into the oven to bake. While the squash is roasting it begins to caramelize down and the prosciutto turns extra crispy.

Butternut Squash and Cheese Stuffed Pasta Shells |

Now that cheese mix

Once the squash has finished roasting set the prosciutto aside. Then combine the squash with the ricotta and fontina cheese. If you’d like to make the cheese mix even creamier, you could puree the squash in a food processor. I just didn’t think it was all that necessary of a step.

From here, you’ll want to stuff your pasta shells with that delicious cheese mix.

Butternut Squash and Cheese Stuffed Pasta Shells |

The marinara sauce

I’ve said this before, but I am a huge fan of using store-bought marinara sauce. Especially if you can find yourself an awesome brand like Mezzetta. Mezzetta is a brand that’s been in my kitchen from the time I was a baby to now. My dad used their jarred olives and peppers since before I was born. So their products have always been a staple in my kitchen.

I was so excited when Mezzatta recently released their line of Artisan Ingredients® pasta sauces. I knew they’d soon become pantry staples for me. My favorites are their Italian Plum Tomato Marinara and their Spicy Italian Plum Tomato Marinara – which is what I used in today’s pasta.

Butternut Squash and Cheese Stuffed Pasta Shells |

It’s the simplest blend of tomatoes, garlic, and herbs. The spicy version has Calabrian chili peppers added, which we all LOVE.

Spoon the marinara sauce into a baking dish, add the stuff shells, a little more marinara, and top with cheese. Then just bake until the pasta is golden and the cheese has melted.

Hello to cheesy butternut squash pasta perfection.

The butternut squash lends a creamy texture to the cheese mix and the marinara sauce adds classic Italian flavors. The combination together is perfect for fall!

One of my new favorite fall recipes!

Butternut Squash and Cheese Stuffed Pasta Shells |

Looking for September pasta recipes? Here are a few ideas: 

Butternut Squash Pasta Carbonara with Rosemary Bacon

Creamy Butternut Squash Alla Vodka Pasta

Roasted Butternut Squash and Spinach Lasagna

Lastly, if you make these Butternut Squash and Cheese Stuffed Pasta Shells,  be sure to leave a comment and/or give this recipe a rating! Above all, I love to hear from you guys and always do my best to respond to each and every comment. And of course, if you do make this recipe, don’t forget to tag me on Instagram! Looking through the photos of recipes you all have made is my favorite!

Butternut Squash and Cheese Stuffed Pasta Shells

Prep Time 30 minutes
Cook Time 45 minutes
Total Time 1 hour 15 minutes
Servings: 6
Calories Per Serving: 813 kcal

Nutritional information is only an estimate. The accuracy of the nutritional information for any recipe on this site is not guaranteed.



  • 1. Preheat oven to 425° F. On a baking sheet, toss together the olive oil, butternut squash, thyme, and a pinch each of red pepper flakes, salt, and pepper. Lay the prosciutto over the squash. Bake for 15-25 minutes, until the prosciutto is crispy. Remove the prosciutto and set aside. If squash needs more time, return to the oven for another 10 minutes, or until the squash is tender.
    2. Meanwhile, bring a large pot of salted water to a boil. Boil the pasta until al dente according to package directions. Drain.
    3. In a medium bowl, combine the ricotta, fontina, and roasted butternut squash. Season with salt and pepper.
    4. To assemble, spoon 2-3 cups marinara sauce into the bottom of a 9×13 inch baking dish. Stuff each shell with 1 tablespoon of the cheese and place into the baking dish with sauce. Top with the remaining marinara sauce and mozzarella. Bake 20-25 minutes or until the cheese has melted and is lightly browned on top.
    5. Serve the shells topped with prosciutto and basil. Enjoy!
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Butternut Squash and Cheese Stuffed Pasta Shells |

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    1. Hey Melissa,
      Totally! Just make up until the point of baking, cover and pop in the fridge, and then bake as directed. Please let me know if you give the recipe a try, I hope it turns out amazing for you! xTieghan

    1. Hi Ruth,
      You will want to peel the squash as you are cubing it. I hope you love the recipe, please let me know if you give it a try! xTieghan

  1. We love this dish- it’s part of our rotation! Question: do you think I could freeze it.. after assembly, but before baking? (Prepping for the arrival of twins) thanks!

    1. Hey Cheryl,
      Thank you so very much for giving this recipe a try, I love to hear that it was enjoyed! Yes, I think that would work well for you! Happy Holidays!??

  2. 5 stars
    Awesome flavors that got even better as leftovers (I cooked for 2, otherwise there wouldn’t have been any). I did puree the butternut squash and used a piping tube. It was worth all the effort. Your photography is awesome BTW.

    1. Hey Angie,
      Wonderful! Love to hear that this recipe was a hit, thanks for making it! Have the best week:) xTieghan

  3. 5 stars
    So delicious. My store was out of jumbo shells, but manicotti was a great sub. I also used your slow cooker marinara that I had in the freezer. I love that marinara! Another HBH dinner winner!

  4. 2 stars
    also the recipe notes a temperature for roasting the squash but doesn’t provide a temperature for cooking the assembled dish.

  5. 2 stars
    the filling was nice but the sharpness of the marinara sauce overwhelmed the softer more subtle interaction of the roasted squash and fontina cheese. will keep the squash/cheese/ricotta recipe and keep looking for a sauce that compliments instead of drowns out the flavors.

  6. 5 stars
    We really enjoyed this! I prepped it early in the day, then let sit at room temp for about 30 minutes before baking it off. The prosciutto on the top was a tasty addition. Our guests asked for the recipe!

  7. Can you make this dish a day early for a dinner party the next day? What’s your advice on storing and reheating?

  8. You say “set aside prosciutto” – but then you never come back to it. Usually when a recipe says to “set aside” an ingredient, it gets added back into the recipe at some point. Good prosciutto is too expensive and delicious to throw away… what happens to the prosciutto in this recipe?

    1. Hi there, so sorry for the confusion! The prosciutto is used as a crispy topping, I usually bake mine in the oven to crisp it up and add to my pastas! Enjoy 🙂 xTieghan

  9. 5 stars
    Unreal! The cheese mixture with the butternut squash smells so incredible, like a sweet dessert you could eat on toast! This dish is so delicious, and it honestly didn’t take too long once squash was all prepped. A favorite!

  10. 5 stars
    Family enjoyed it a bunch. I wasn’t sure how the butternut squash and tomato sauce would pair – surprisingly well!