This post may contain affiliate links, please see our privacy policy for details.

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!
View Recipe Comments
Butternut Squash and Cheese Stuffed Pasta Shells |

Add a Comment

Recipe Rating

This site uses Akismet to reduce spam. Learn how your comment data is processed.


  1. 5 stars
    Update: Made this last night.

    Adjustments I made:
    Doubled the butternut squash (per comments ppl made)
    Omitted prosciutto.
    Added ground beef and mild Italian sausage to the red sauce (I needed a bump of protein).
    Added two leaves of chopped sage (it looked like there was sage in the picture, so I went for it).

    It. Was. Absolutely. Delicious.

    My 10yr old kids devoured it, and I’m pretty sure my husband went for thirds!

    Thank you for sharing this recipe Tiegan! (found it on Pinterest when searching “butternut squash dinner recipes”

    1. Hey Ali,
      Happy Friday!! Thanks so much for trying this recipe and sharing your review, so glad it was a hit! Thanks for sharing all of your notes and what worked well for you! xT

  2. Looking forward to making this but I need a bump of protein. Would Italian sausage & beef in the sauce overpower the other flavors?

    1. Hey Ali,
      I think sausage would be a great addition here! Let me know if you give this dish a try, I hope you love it! xT

  3. 5 stars
    Yummy. It was a big hit and so easy to follow the recipe. I could only find manicotti noddles but they worked great. I served with a side salad and garlic bread to soak up the sauce.

  4. 5 stars
    I absolutely hate cooking and meal planning so I am always very excited to see a recipe that isn’t too hands on with good reviews. This recipe is fantastic. It was simple and the flavor really delivered. The textures of everything combined was truly delightful and leftovers the next day were even better. I already know this recipe is going to be getting made time and time again. Thumbs up from me – I’m autistic, so this is a double win as I struggle with finding foods that meet all expectations.

    I did make a few minor changes as I couldn’t find fontina or provolone here, so I used Gouda which was a nice pop of cheese throughout the dish. I didn’t add the prosciutto. I’m not vegetarian, I just couldn’t justify 7$ for a pack of meat that would essentially be a garnish. I didn’t miss it at all. I used a red wine and basil base for the marinara.

    I think this would be a great dish to hide some additional veggies in as well. I might add peas next time!

    Thank you for sharing your recipe, I have a feeling I will be cooking more of your food in the future!

    1. Oh and I doubled the butternut pumpkin, because I was worried about it getting lost in the sauce (literally)… turned out to be a good choice!

  5. Any tips for freezing a portion to cook for a future weeknight meal? Tasty enough to make the full recipe- but only 2 mouths to feed in this house! 🙂

    1. Hey Annie,
      I would just freeze before baking, should be just fine for you to do! Please let me know if you have any other questions! xx

  6. Outstanding! Changes:
    1. I increased the butternut squash and marinara a bit. The roasting took much longer to get the prosciutto crisp – maybe 45 minutes or more.
    2. I used lactose free Cabot Seriously sharp shredded cheese rather than fontina or provolone, but it truly kicked it up BIG TIME.
    3. I also roasted 1/3 cup of onion and emulsified it with the butternut squash before mixing it into the cheese, then stuffed each shell with 2-3 tablespoons of the mix baking it until the thermometer showed 165 degrees. It probably took 5-10 minutes longer than planned because I over-stuffed the shells.
    4. Everybody was in awe of how good it was. We use a 1-4 star scale in our home, but if something is “over-the-top” we say “serve to guests” and that is where this ended up!

    1. Hey Dennis,
      I appreciate you making this recipe and I’m thrilled to hear that it turned out well for you! Thanks for sharing the adjustments that worked best for you! Have a great weekend! xx

  7. 4 stars
    This was delicious! The butternut squash in the filling was my favorite part of this dish! However, I thought the taste of the squash was masked by the cheese and marinara sauce so next time I would add more squash. Also – I’m not sure where I went wrong but I didn’t have enough of the filling (I used 1 tbs per shell) for 1lb of pasta. I probably had about 4 oz of shells left over. Regardless – this was very easy and tasty!

    1. Hi Sarah,
      Happy Monday! 👻 I am thrilled to hear that this recipe was a winner, thanks so much for making it! Happy Halloween! 🎃

  8. 5 stars
    One of my favorite recipes. My husband who isn’t a fan of pasta loved it! Thank you for all your hard working in creating these recipes for people to enjoy! 10/10! I had enough left over to freeze too so I’ll get to eat them again next week. Woot!

    1. Hi Savanna,
      Perfect! I appreciate you making this recipe and sharing your feedback, I am so glad it was a hit! xx

  9. This looks incredible! I’m curious about the herbs, though. It looks like you also included sage (or ???) with the thyme and pepper flakes in the second photo. Please advise.
    Many thanks, Tieghan, for sharing your fabulous recipes!

    1. Hey Liz,
      It’s actually some basil:) But you can use any fresh herbs that you enjoy for this recipe! I hope you love this dish! xT

    1. Hey Wanda,
      Amazing!! I am so glad to hear that this recipe was enjoyed, thanks so much for making it and sharing your feedback:) Totally, that will work well for you!

  10. 4 stars
    Good concept. I like to putter in the kitchen, taste and smell as I go along, etc. I am not a Master Jedi in the kitchen (that’s my mother) but I am a Jedi 😉


    1) double the amount of squash. I feel there is too much cheese in the mix, and the butternut squash is just “barely there.”

    2) threw in some shallots in with the butternut squash and roasted them together. Gave it some more oomph.

    3) I love Lidia Bastianich’s marinara recipe (very simple, can do in the time it takes to roast the butternut squash), so I made that, tripled the marinara recipe and had just enough left over for anyone who wanted to put extra sauce on top of their serving.

    4) I like stuffing the shells “to the max,” which is roughly 2-3 T “stuffing” per shell. Doubling the amount of squash and a little extra cheese made for stuffing about 2/3 pound of the jumbo shells. Turned out just right because some of the shells were torn/broken. Dragged those pieces through the sauce and munched as I went along (see note above, smelling/tasting food as I go along).

    There weren’t any leftovers 🙂

    1. Hey Leslie,
      Happy Sunday!! So glad to hear that this recipe was enjoyed, thanks so much for making it!! Thanks for sharing your notes and what worked well for you. ? xx

  11. 4 stars
    I couldn’t find any large pasta shells at the supermarket so I actually made with lasagna sheets and spread ricotta/pumpkin mix on the sheets. Then did tomato at the bottom, the middle layer and then over the top. This did require a extra bit of sauce though. Really yummy, easy eating.

    1. Ooo and I also added mushroom, onion and Courgette to the marinara sauce for extra veg. Just cooked before hand in fry pan to soften!

    2. Hi Megan,
      Fantastic!! I love to hear that the recipe was enjoyed, thanks for giving it a try. Have the best week:)) xT

  12. 5 stars
    Sitting in front of a plate of these shells left over from last night, and couldn’t be happier! My kids are SUPER picky, and they all ate this with no problems. They would never suspect the squash was in them, I mashed it to make it blend with the ricotta into a cream. I didn’t see that step in the recipe, but that’s what I chose to do. My son asked for the recipe to be added to our weekly rotation, and I’m in agreement. It really is a comforting recipe, the balance of flavor is great!

    1. Hey Brandi,
      Wonderful!! Thanks so much for making this recipe, I love to hear that it was a winner. Have the best weekend:) xT

      1. 5 stars
        Just tried this recipe tonight and it was absolutely delicious! The ingredients come together in a beautiful combination that hits all the taste buds! Super easy to make and we all loved it. I will definitely make this again!! ?

      2. So are you supposed to mash the squash? I want to make this; it looks delish. Came here to the comments looking for that answer.

    2. I have made this a few times and honestly it’s AMAZING. My family keeps requesting this. Just a note- I use a box of jumbo shells (12 ounce) and still have some shells leftover (maybe I overstuff them ;))so either make more of the butternut/cheese stuffing or plan to use a little under 12 ounces of shells. This recipe is perfection!!!

      1. Hi Roxanne,
        Awesome!! I love to hear that this recipe was enjoyed, thanks a lot for giving it a try! xx