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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

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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

Butternut Squash and Cheese Stuffed Pasta Shells | halfbakedharvest.com
4.31 from 376 votes
6
calories 813kcal
Prep30 minutes
Cook45 minutes
Total1 hour 15 minutes
Best for nights when you’re craving Italian, but also craving those cozier fall flavors!
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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!

Nutrition

Calories: 813kcal

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

Did you make this recipe? Please rate & comment below.

Butternut Squash and Cheese Stuffed Pasta Shells | halfbakedharvest.com

Meet Tieghan Gerard

I'm Tieghan, the recipes you'll find here are inspired by the people and places I love most. I try to live simply, eat seasonally, and cook with whole foods. My hope is to inspire a love for amazing food, as well as the courage to try something new!

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4.31 from 376 votes (319 ratings without comment)

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199 Comments

  1. Stephanie Morgan says:

    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. halfbakedharvest says:

      Hey Stephanie,
      Happy Sunday! I am thrilled to hear that this recipe was enjoyed, thanks a lot for making it! xTieghan

  2. Theresa says:

    Made this last night, might be the best thing I’ve ever made! Thank you for this amazing recipe.

    1. halfbakedharvest says:

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

  3. Ellie says:

    I can’t find any jumbo shells! Would manicotti shells work?

    1. halfbakedharvest says:

      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

  4. Mindy says:

    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. halfbakedharvest says:

      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

  5. Sylvia lennon says:

    Made this last night ( stuffed shells with cheese and butternut squash) it was delicious!

    1. halfbakedharvest says:

      Hey Sylvia,
      Happy Friday!! I am thrilled that this recipe was a winner, thanks so much for giving it a try! xTieghan

  6. Emily M Jansen says:

    Was thinking the same

  7. M R says:

    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!

    1. Emily M Jansen says:

      Was thinking the same

    2. halfbakedharvest says:

      I hope you love the recipe!!

  8. Emma says:

    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. halfbakedharvest says:

      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

  9. Lindsay says:

    5 stars
    This looks amaaaaaazing!! Making it asap. Also, Happy Birthday!!

    1. halfbakedharvest says:

      Thanks Lindsay! I hope you love the recipe!! xTieghan

  10. Judy says:

    The other herb looks like basil???

    1. halfbakedharvest says:

      Hey Judy,
      I used some sage, basil is great too, really any herbs you like will work! xTieghan

  11. Kiki says:

    What would be a good substitute for the ricotta? I have someone who doesn’t like it:(

    1. halfbakedharvest says:

      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

  12. suzan says:

    how much pasta does this need? it isn’t included in the ingredients list.

    1. Leah Porter says:

      It says 1 pound 🙂

    2. halfbakedharvest says:

      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

  13. Linda Harris says:

    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. Linda W says:

      Looks like fresh thyme to me!

    2. halfbakedharvest says:

      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

  14. S Weiss says:

    Could you use a white sauce?

    1. halfbakedharvest says:

      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

  15. Colleen Wilson says:

    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. halfbakedharvest says:

      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