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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. MK says:

    Hi T,
    Looking to make this weekend for friends. Is it possible to make a day ahead refrigerate and bake the final product after guests arrive? Would the dish be compromised in anyway?

    1. Tieghan Gerard says:

      Hey there! Yes, that should work just fine! 🙂 xTieghan

  2. Matt says:

    5 stars
    Great recipe! Don’t skip the prosciutto. Extra yummy flavor to offset the creamy cheese.

    1. Tieghan Gerard says:

      Hey! This is awesome, I’m so happy to hear this recipe turned out the way you’d hoped! 🙂 xTieghan

  3. Courtney says:

    The photos look like you used sage in the recipe? If so how much.

    1. Tieghan Gerard says:

      Hi there! I usually like to use some sage in my pasta, but it’s up to you if you want to use it! 🙂 xTieghan

  4. Debbie says:

    5 stars
    This was delicious!

    1. Tieghan Gerard says:

      Hi there! Thanks so much for giving this recipe a try, I’m so glad you enjoyed it! xTieghan

  5. Shannon says:

    5 stars
    Tasty

    1. Tieghan Gerard says:

      Thank you so much Shannon 🙂 xTieghan

  6. Amy says:

    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. Tieghan Gerard says:

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

  7. Suzi says:

    Yummy!
    Loved this one and so did the family
    I’m not sure how to add a photo?

  8. Danielle Oris says:

    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!

  9. Julia says:

    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

  10. Emily says:

    Sounds fabulous! Do you think this would work with manicotti? Maybe if it blended and was piped in?

  11. Melissa says:

    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!

  12. Betsy says:

    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”!

    1. Tieghan Gerard says:

      Hi there! I’m glad you enjoyed this recipe, and I agree about the prosciutto! 🙂 xTieghan

  13. Heather says:

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

    1. Tieghan Gerard says:

      Hi there! Thanks so much for trying out this recipe! So glad you enjoyed it 🙂 xTieghan

  14. Jamie Sletten says:

    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.

  15. Taylor says:

    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!