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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 | halfbakedharvest.com

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 | halfbakedharvest.com

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 | halfbakedharvest.com

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 | halfbakedharvest.com

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 | halfbakedharvest.com

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 | halfbakedharvest.com

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: 414 kcal

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

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Ingredients

Instructions

  • 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!
Butternut Squash and Cheese Stuffed Pasta Shells | halfbakedharvest.com

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Comments

  1. 5 stars
    This is delicious!!! I agree with a lot of the reviews. Add more squash! I will definitely make this again, it was a huge hit!

    1. Hey there! Thanks so much for giving this recipe a try, I’m so glad you enjoyed it! Have a lovely week! xTieghan

  2. 5 stars
    Sooo delicious! I love cooking and trying new recipes. I made this for every one on vacation and they loved it. Thank you!

  3. 5 stars
    I love this recipe! Made it twice now. I don’t eat prosciutto and I didn’t find the recipe lacking at all without it! Yum

  4. 5 stars
    Made these last night for my butternut squash loving friend. I did decide to do a mix of ricotta and goat cheese instead of fontina and LOVED it! Used Rao’s Arrabiatta sauce. So amazing! Thank you!

  5. 4 stars
    Cooked it and hmm – I admit, I don’t think I’d recommend it without the prosciutto. Not that a bite without the prosciutto is BAD, but it definitely is what elevates it from “fine” to “great”!

  6. This was fantastic! I added fresh baby spinach to the cheese mixture for an extra veggie and color. The whole family loved it!

  7. 3 stars
    I thought this was ok. I didn’t feel like the butternut squash and prosciutto was necessary and that was the part I was excited about! Like it needed to choose between butternut squash flavors and marinara. Hubby agreed. Was an easy and pretty quick recipe to make with a sleeping baby in the other room.

  8. 5 stars
    My husband and I took a trip to Italy two years ago, and this is the first recipe we’ve found that reminds us of our trip! SO tasty!

  9. 5 stars
    I made these shells last night and they turned out great! Covered them during cooking for the first 15-20 minutes and then broiled them for a few minutes at the end to brown the cheese. My husband loved this recipe and he isn’t usually a squash fan – he may not have even known the butternut squash was in there! Definitely being transferred to the recipe box to make again. Thanks!

    1. Hi Kara,
      Happy Sunday!! I am delighted to hear that this recipe was enjoyed, I truly appreciate you giving it a try! xTieghan

  10. 5 stars
    Hello Tieghan,
    I love all your recipes. Quick question? would it work roasting frozen squash vs fresh?
    thanks so much

    1. Hey Jeanne,
      Yes, frozen squash would be just fine to use here. I hope you love the recipe, please let me know if you give it a try! xTieghan

  11. 5 stars
    Made this tonight, so good!! Both my 10 month old and 3 year old devoured it and wanted seconds! Thanks for such a great recipe!

  12. 5 stars
    This was a crowd pleaser! Tiegan, I always love your recipes and cook them every week. This one was especially great. I added more spices and kept the lid on while simmering as other reviewers suggested. My son and husband love hamburger helper (not I) and they loved this more plus I did too! such an easy, healthy one pot week night meal. Thank you!!!

  13. 5 stars
    I loved the use of the squash mashed in the ricotta filing! I’ve always just added roasted squash to the sauce. This time I even added leftover pumpkin into the filling. My husband (who isn’t the biggest pasta/squash fan) went back for seconds! I made a homemade beef bolognese sauce but jarred sauce would work well too 🙂
    Squash/pumpkin with tomatoes are the best fall pairing in my opinion!

  14. 5 stars
    This was fantastic! We felt like it was just enough squash, but if you want it more pronounced, then add more. The crisped prosciutto pieces were also an amazing touch. So glad I don’t need to cook for a few nights now. Would also be great for a group.

    1. Hey Jen,
      Fantastic!! So great to hear that you enjoyed this recipe and thanks a lot for making it. Have a great week!🍂 xTieghan

  15. 5 stars
    This was amazing! Such a great meal to get in the mood for fall. My filling didn’t quite make enough for a full pound of shells (more like 12 oz), and I needed a second small baking dish to fit the shells and a little extra marinara to drizzle over them. But the taste was fantastic! Will be making this one again. Thanks for another wonderful recipe!

    1. Hi Annie,
      Fantastic!! So great to hear that you enjoyed this recipe and thanks a lot for making it. Have a great week!🍂 xTieghan

  16. Just made this today. Very good. The spicy sauce has a lot of heat. But since I always make my own sauce this was good for a jar sauce. 🤫 don’t tell the husband since he hates jar sauce. He liked the meal as well. I bought one jar of sauce which seemed ok but could of used slightly more. I would recommend a jar and a half. I also would use more squash. Personal preference there. Made the fall harvest salad to go with it . That was also good. Plan on making that for my lunch for the week. Thanks for another good recipe

    1. Hi Christine,
      Fantastic!! So great to hear that you enjoyed this recipe and thanks a lot for making it. Have a great week!🍂 xTieghan

  17. Hi Tieghan, I love your recipes! I usually find great ones on line, but I also sell your cookbooks in my Kitchen shop 🥰
    I’m going to make this butternut shell recipe for company this weekend….but I’m looking to serve it as a side. What would you recommend? Roasted pork tenderloin or maybe some roasted sausages? I’d love to hear your ideas.
    Thanks,
    C

  18. 4 stars
    Made this last night for some friends – it was really good! I found myself wanting more of that squash flavor though so I think next time (cause there will DEFINITELY be a next time!), I’ll do more like 3.5-4 cups of butternut squash and less ricotta and provolone for the filling. Can’t wait to try more recipes!

    1. Hey Kelsey,
      Fantastic!! So great to hear that you enjoyed this recipe and thanks a lot for making it. Have a great week!🍂 xTieghan

  19. 5 stars
    This is one of the best dinners I have prepared recently!! And the amount of leftovers is great.
    I made a few additions:
    1. Added one clove minced garlic and some chopped fresh basil to the ricotta mixture.
    2. Chopped up the crispy prosciutto and added it to the ricotta mixture as well.
    Delicious

    1. Hey Amanda,
      Love to hear that this recipe was enjoyed, thanks a bunch for making it! Have the best weekend🍁 xTieghan

    1. Hey Julee,
      Love to hear that this recipe was enjoyed, thanks a bunch for making it! Have the best weekend🍁 xTieghan

    1. Hey Lauren,
      For this recipe, I would recommend boiling the noodles first:) I hope you love the recipe, please let me know if you give it a try! xTieghan

    1. Hey Megan,
      I would probably just use your favorite Alfredo sauce. I hope you love this recipe, please let me know if you give it a try! xTieghan

    1. 5 stars
      So so good! Everything I cook is from half baked and every time it turns out perfect and even better than I would’ve thought! I absolutely loved this recipe!

    2. Hey Stephanie,
      Nope, I did not, you can follow the recipe as written:) Please let me know if you give it a try! xTieghan

  20. 5 stars
    Big hit! Delicious, easy to follow recipe that is full of flavour! Already in rotation for dinner next week again. I find it easier to cut squash in half, season, cook it and then scoop out food to mix with the cheese than to cut into cubes.

    1. Hey Sharon,
      I used both sage and thyme in this recipe:) I hope you love the dish, please let me know if you give it a try! xTieghan

  21. 5 stars
    This was so yummy! I made it vegetarian and it was still delicious. I’ve made two of your recipes so far this week and both have been very well received. Thank you!!

  22. 4 stars
    We loved this recipe! I blended the squash in the food processor and then folded in the cheese (schitts creek pun intended!). My boyfriend doesn’t like squash so by doing this and using a sharp provolone he couldn’t even taste it! I did 16 ounces of jumbo shells but ended up with 4 ounces left over because I couldn’t squeeze anymore in to the 9×13 pan. I ended up broiling the top at he end to get the mozzarella a little crispy. The prosciutto on top is such a nice, crispy addition. Will definitely make again!

        1. Hey Stephanie,
          I did not, you can follow the recipe as is:) Please let me know if you have any other questions! xTieghan

  23. 5 stars
    This recipe was omg delicious! I roasted Italian chicken sausage along with the butternut squash to add a meat protein for my hubby and it was a hit. Thanks Tieghan for another amazing recipe!

  24. 5 stars
    So easy! And restaurant quality. Would order it again and again if it was on a restaurant menu.
    Cooked this with your lemon shrimp recipe. Enjoyed every bite.

  25. 5 stars
    Really delish and surprisingly easy to make! I used an aged fontina that had a sharper taste and it worked really well with the sweetness and creaminess of the cheeses. The spicy marinara, salty prosciutto and fresh basil is the perfect balance.

  26. 5 stars
    Amazing!!! Going to be a staple in our home. We turned it into a lasagna because that’s what we had available. So so good.

    1. Hey Sarah,
      I would add fully cooked sausage or chicken to the dish. I hope you love the recipe, please let me know if you give it a try! xTieghan

  27. I’d love to make this but need to use gluten free noodles. I haven’t found gluten free shells yet. Any recommendation which type of noodle could work with this?

    1. Hey Renae,
      You could do GF lasagna noodles and just roll them up:) I hope you love this recipe, please let me know if you give it a try! xTieghan

  28. Made this tonight and it was a winner! I made half a recipe for the 2 of us so have leftovers. Can I freeze them? I have saved several of your recipes and am anxious to make others.

    1. Hey Carol,
      Happy Sunday! I am thrilled to hear that this recipe was enjoyed, thanks a lot for making it! Yes, totally fine to freeze the leftovers. xTieghan

  29. 5 stars
    I made this last night celebrating my husband and I’s 17th wedding anniversary. Absolutely wonderful!!! The recipe is a keeper !! Thank you sharing the recipe.

    1. Hey Theresa,
      Awesome! I am so glad to hear that this recipe was enjoyed, thanks for making it! Have the best weekend! xTieghan

    1. Hey Elle,
      Sure, manicotti would also work well here. I hope you love this recipe, please let me know if you give it a try! xTieghan

  30. I would like to make this with gluten free pasta. Stuff shells are not available gluten free. Could this be made with a different shape pasta and not be stuffed?

    1. Hey Mindy,
      You could use GF lasagna noodles and roll them up:) I hope you love this recipe, please let me know if you give it a try! xTieghan

  31. This dish seems like it might go even better with a non-tomato jarred sauce. If I give this a go I might opt to try with a pumpkin or white sauce. Something about butternut squash doesn’t seem to work with tomato for me. But the filling looks amazing!

  32. I’m excited to try this! Could it be assembled the night before prior to baking? Would it freeze well if frozen before it was baked?

    1. Hey Emma,
      Yes, both of those options would work well for you. I hope you love this dish, please let me know if you have any other questions! xTieghan

    1. Hey Kiki,
      You could use mascarpone or a light whipped cream cheese. I hope you love this recipe, please let me know if you give the recipe a try! xTieghan

    1. Hey Suzan,
      The recipe calls for 1 pound of jumbo pasta shells. I hope you love this recipe, please let me know if you give it a try! xTieghan

  33. Dear Tieghan,

    This recipe looks amazing. Can’t wait to try it! In the photo you’ve added another herb, cut in a tiny julienne. Can’t tell what it is. Sage, maybe? The mor herbs the better as far as I’m concerned.

    Thanks,
    Linda

    1. Hey Linda,
      Yes, I also used some sage here. I hope you love this recipe, please let me know if you give it a try! xTieghan

    1. Hey there,
      Yes, that would also be great! I hope you love this recipe, please let me know if you give it a try! xTieghan

  34. Hi Tieghan! I am loving the look of these stuffed shells! Question..in the photo of the cubed squash, what other her. Do you have shopped up on there? To me it looks like sage (maybe?), but it isn’t listed as an ingredient. I can see the thyme, but not sure what else is on there. Also, another pretty good show to watch is called The White Lotus.

    1. Hey Colleen,
      I have some sage on there as well! I hope you love the recipe, please let me know if you give it a try! xTieghan