Pumpkin Cheese Stuffed Shells Bolognese Bake…the perfect warming dinner to welcome the start of autumn. It’s the coziest pumpkin pasta bake! Jumbo pasta shells stuffed with pumpkin, cheese, and fresh sage. Then baked in a spicy Bolognese style red sauce that’s saucy, a touch spicy, creamy, and so delicious! This is a great fall pasta to serve any night of the week, or for your next gathering with family or friends.

overhead photo of Pumpkin Cheese Stuffed Pasta Bolognese Bake

And just like that, we have our very first pumpkin recipe of the fall season! Did I think the first pumpkin recipe would be a savory one? No, but it’s ok because we have something sweet coming tomorrow. You guys, I am so excited it’s fall!

I touched on this a bit yesterday, but this fall feels even more special than years past. I think we can all agree that this year has been weird, to say the least. It started out amazing with the HBH Super Simple cookbook tour still going strong and then things just, ahh…went weird. And at times definitely difficult. But hopefully we’re all making it through. And because of the very bizarre year we’ve had, this fall just feels like it’s going to be good.

I’m excited to actually be home this fall and not traveling from one place to the next. Sure I love a busy fall travel season, but I can also love a fall cozied-up at home even more. So you see, my mind is full of so many cozy fall recipes…including plenty of new pumpkin recipes.

And it’s all starts with this bolognese bake.

Pumpkin Cheese Stuffed Pasta Bolognese Bake | halfbakedharvest.com

The story.

Oh, this bake. It started out as something completely different, but somehow, someway, my mind turned it into this delicious bake you’re looking at today.

Originally there was no pumpkin, no pasta shells, and instead, there was really just Bolognese sauce baked with pasta. But guys, this felt boring. It needed something more. Something to make it special enough for this time of year (yes, I’m cheesy, go with me on this). So then I kept thinking…and thinking. Once I really start to think on a recipe, there’s just no stopping my brain.

Pumpkin Cheese Stuffed Pasta Bolognese Bake | halfbakedharvest.com

I toss around idea after idea until I land on something I LOVE.

After a good amount of thinking, I finally came to this bake. It’s nothing close to your average pasta bake, but it sure is delicious.

overhead photo of Pumpkin Cheese Stuffed Pasta Bolognese Bake

The details.

This one is simple. But you do need some time to allow the sauce to simmer, and then for the pasta to bake. No more than an hour though, so this still makes for a great weeknight dinner.

To start, make the spicy, saucy, creamy, Bolognese sauce. This sauce is so good. Actually, in my dad’s words, “THIS SAUCE IS SO GOOD”. That’s coming from a man who’s constantly telling me he does not like meat sauces. So you should know…this one is special. It’s a simple mix of ground chicken (or beef), herbs, and spices. The key is to use a touch of fennel seeds and a bit of smoky paprika to really add some flavor. Next toss in some jarred tomatoes and a splash of white wine. Then let the sauce simmer for a bit to thicken up.

overhead close up photo of Pumpkin Cheese Stuffed Pasta Bolognese Bake

While the sauce simmers, make the stuffed shells. These sells are almost too good…warming pumpkin, fontina cheese, and fresh chopped sage. All stuffed into a pasta shell. Nothing not to love here.

I also added a little crumbled blue cheese, which I love. But if you’re one of those people who despise blue cheese, just omit it.

Ok, next, snuggle the pumpkin stuffed shells right into the Bolognese sauce, then top with provolone, and bake until the pasta is golden and the cheese has melted.

Hello to cheesy, pumpkiny pasta perfection.

overhead photo of Pumpkin Cheese Stuffed Pasta Bolognese Bake on dinner plate

This is one of the best dishes to come out of my kitchen as of late. That is a bold statement, but you guys, these stuffed shells are the perfect fall comfort food. Every last bite is a delicious one. My whole family really loved this meal.

I know it may seem a little odd to use pumpkin in such a savory way, but go with me on this one. The pumpkin lends a creaminess to the stuffed shells while providing a hint of both sweetness and autumn flavors. And when paired with that hearty Bolognese sauce?

Beyond delicious! Please give this one a try! You’ll love it, and your family will love you for making it!

overhead close up photo of Pumpkin Cheese Stuffed Pasta Bolognese Bake

Looking for other fall pasta recipes? Here are a few ideas: 

Pumpkin Cauliflower Gnocchi with Nutty Browned Butter and Whipped Ricotta

Butternut Squash Pasta Carbonara with Rosemary Bacon

Slow Cooker Red Wine Sunday Ragù Pasta

Brown Butter Brussels Sprout and Bacon Ravioli

Lastly, if you make this pumpkin cheese stuffed pasta shell bolognese bake, 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!

Pumpkin Cheese Stuffed Pasta Bolognese Bake | halfbakedharvest.com
4.14 from 375 votes

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

The Recipe

Pumpkin Cheese Stuffed Pasta Shell Bolognese Bake

The perfect warming dinner to cozy-up to and welcome the start of autumn!

Prep Time 20 minutes
Cook Time 40 minutes
Total Time 1 hour
Servings 8
Calories 492 kcal



  1. 1. Preheat the oven to 400 degrees F. Lightly grease a 9x13 inch baking dish or a dish of similar size.

    2. Heat the olive oil in a large pot over high heat. When the oil shimmers, add the onion and cook 3-5 minutes. Add the meat, garlic, oregano, fennel, paprika, red pepper flakes, and a pinch each of salt and pepper. Cook until browned all over, about 5 minutes. Reduce the heat to low, add the marinara and wine. Simmer for 15 minutes or until the sauce thickens slightly. Taste and adjust seasonings as needed.

    3. Meanwhile, bring a large pot of salted water to a boil over high heat and boil the pasta until al dente according to package directions.

    4. In a medium bowl, combine the pumpkin, fontina, blue cheese (if using), sage, nutmeg, and a pinch each of salt and pepper.

    5. To assemble, spoon 3/4 of the Bolognese sauce into the bottom of the prepared baking dish. Working with one pasta shell at a time, spoon about 1 tablespoon of the pumpkin cheese mix into each shell, placing the filled shell into the baking dish as you go. Spoon the remaining Bolognese sauce over top of the shells. Add the provolone.

    6. Transfer the baking dish to the oven and bake 20-25 minutes or until the cheese has melted and is lightly browned on top. Serve topped with fresh oregano.

Recipe Notes

To Make Vegetarian: no problem, just omit the meat. No other changes needed.

To Make Ahead: complete the recipe through step 5. Let cool, and store in the fridge until ready to serve!

overhead horizontal photo of Pumpkin Cheese Stuffed Pasta Bolognese Bake