Name: Pumpkin Pesto Cheese Stuffed Shells Recipe
Prep time: 20 min
Cook time: 25 min
Total time: 45 min
Cuisine: Italian-American
Ingredients: 2 tablespoons extra virgin olive oil; 1/2 pound ground chicken sausage; 1 red bell pepper, chopped; 1 cup pumpkin puree; 1/2 cup vodka; 1 cup whole milk; 2 teaspoons dried oregano; 1 pinch crushed red pepper flakes; Salt and pepper to taste; 1 pound jumbo shells; 16 ounces whole milk ricotta cheese; 2 cups shredded fontina cheese; 3/4 cup basil pesto (divided into 1/2 cup and 1/4 cup); 8 ounces shredded mozzarella cheese; Fresh basil, for serving

Jump to Recipe· 4.8 from 17 reviews

Oh, I’m so excited to share this Pumpkin Pesto Cheese Stuffed Shells Recipe with you! It’s one of those dishes that feels cozy and special all at once, perfect for a chilly night when you want comfort food but also something a little fancy. The mix of creamy ricotta, savory chicken sausage, and that unexpected pumpkin-pesto blend makes this meal stand out from the usual pasta routine.

What I love most about this recipe is how it balances unique flavors with familiar, comforting textures. It works beautifully for weeknight dinners but also shines when you’ve got guests over and want to impress without sweating over something complicated. Plus, the pumpkin adds a subtle sweetness and richness that pairs so well with the herbs and cheese, making every bite memorable.

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Why This Recipe Works

Balanced Flavor Profile: The pumpkin and pesto create a unique, harmonious blend of sweet, savory, and herbal notes.
Creamy & Satisfying: The combination of ricotta, fontina, and mozzarella melts beautifully for a rich, indulgent texture.
Easy to Prepare Ahead: You can assemble the dish in advance and bake it when you’re ready, perfect for busy days.
Versatile for Occasions: Whether it’s a family dinner or holiday gathering, this recipe adapts effortlessly.

A glass baking dish filled with three layers of food. The bottom layer is a yellowish sauce with some texture, the middle layer consists of white melted cheese that is browned and bubbly in spots, and the top layer has fresh green basil leaves scattered over the cheese. The dish sits on a white marbled surface. photo taken with an iphone --ar 4:5 --v 7

Ingredients & Why They Work

Each ingredient in the Pumpkin Pesto Cheese Stuffed Shells Recipe plays a special role to create a dish that’s both flavorful and comforting. Shopping for quality components, like fresh basil pesto and whole milk ricotta, really elevates the final result.

Extra virgin olive oil: Adds richness and helps brown the sausage for depth of flavor.
Ground chicken sausage: Lean protein that’s flavorful without overpowering the delicate pumpkin and pesto.
Red bell pepper: Provides a touch of sweetness and crunch that balances the creamy filling.
Pumpkin puree: The star ingredient that adds a velvety texture and subtle autumnal sweetness.
Vodka: Helps mellow and blend the sauce flavors—a splash goes a long way.
Whole milk: Enhances creaminess without being too heavy.
Dried oregano: Lends an earthy, herby note to complement the pesto.
Crushed red pepper flakes: Adds just a hint of heat to awaken the palate.
Jumbo pasta shells: The perfect vessel to hold the cheesy pumpkin filling.
Whole milk ricotta cheese: Creamy and mild, providing a smooth base for the stuffing.
Shredded fontina cheese: Melts well and introduces a subtle nuttiness.
Basil pesto: Bursts of fresh herbal flavor that brighten the rich pumpkin crema.
Shredded mozzarella: Creates a gooey, golden topping that everyone loves.
Fresh basil: A final flourish that brings freshness and color to the plate.
Salt and pepper: Essential seasonings to balance and enhance all the flavors.

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Note: You’ll find the complete list of ingredients, along with their exact measurements, in the printable recipe card at the bottom of this post.

Tweak to Your Taste

I love playing around with this Pumpkin Pesto Cheese Stuffed Shells Recipe depending on the season or who I’m cooking for. Feel free to swap ingredients to make it your own—there’s plenty of room to customize without losing the soul of the dish.

Variation: For a vegetarian version, try omitting the chicken sausage and adding sautéed mushrooms or spinach for extra earthiness.
Dairy-Free Option: Use plant-based ricotta and mozzarella alternatives, and swap the pesto for a nut-free version if needed.
Spice it Up: If you like more heat, add extra crushed red pepper or top with a drizzle of spicy chili oil before serving.
Seasonal Twist: Swap pumpkin puree for butternut squash puree in the warmer months for a slightly different flavor profile.

Step-by-Step: How I Make Pumpkin Pesto Cheese Stuffed Shells Recipe

Step 1: Brown the Sausage & Build Your Sauce

Start by heating your olive oil in a large pot over medium-high heat. I like to get the sausage nice and browned—that locks in flavor and gives the dish a meaty depth. Once browned, reduce the heat and add the chopped red bell pepper, then stir in your pumpkin puree. Next, pour in the vodka and whole milk, sprinkle the oregano and crushed red pepper flakes, and season with salt and pepper. Let this simmer gently for 15 minutes. The sauce will thicken slightly as the flavors meld together—make sure you keep it at a low simmer to avoid scorching.

Step 2: Prep the Pasta Shells

While the sauce thickens, get your jumbo pasta shells cooking according to package instructions. I find it best to cook them just until al dente because they’ll keep softening in the oven. Once cooked, drain and rinse under cold water to stop the cooking process and make them easier to handle when stuffing.

Step 3: Mix the Cheese Filling

In a medium bowl, combine the whole milk ricotta, shredded fontina, and half of your pesto. This mix is the creamy heart of the dish and balances the pumpkin sauce beautifully. Give it a good stir until everything is well mixed and creamy.

Step 4: Assemble the Shells

Grease a 9×13 inch baking dish lightly, then spread about three-quarters of the pumpkin sauce on the bottom. Spoon about a tablespoon of the cheese mixture into each shell—don’t be shy here, the filling makes the dish. Stand the stuffed shells up next to each other in the baking dish. Once all shells are filled and arranged, spoon the remaining pumpkin sauce evenly over them. Drizzle the remaining pesto over the top, and sprinkle with shredded mozzarella for that perfect golden finish.

Step 5: Bake to Gooey Perfection

Bake uncovered at 350°F for about 20-25 minutes, until the mozzarella melts and turns lightly golden. Keep an eye on it toward the end—when the cheese has that delicate brown tint and everything is bubbling, you’re done. Let it rest for five minutes before serving to let everything set up nicely.

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Pro Tips for Making Pumpkin Pesto Cheese Stuffed Shells Recipe

Slow Simmer the Sauce: Letting the pumpkin and spices gently reduce deepens the flavor and prevents watery sauce.
Don’t Overcook Your Pasta Shells: Rinse them after boiling to stop carryover cooking and keep their shape during baking.
Use Fresh Pesto: Fresh pesto brightens the dish in ways bottled just can’t match.
Let It Rest Before Serving: Giving the baked shells a few minutes lets the sauce thicken slightly and makes serving easier.

How to Serve Pumpkin Pesto Cheese Stuffed Shells Recipe

This image shows a close-up of a cheesy pasta dish in a white bowl on a white marbled surface. The dish has several layers: at the bottom, there are large pasta shells coated in a creamy, yellowish sauce. Above that is a thick layer of melted cheese with a golden and slightly browned texture on top, giving a rich, bubbly look. Small green basil pieces are scattered on the cheese for color contrast. A fork is lifting some pasta shells covered in the sauce and cheese layers, showing the dish's creamy inside. Photo taken with an iphone --ar 4:5 --v 7

Garnishes

I always top these stuffed shells with fresh basil leaves—there’s nothing like that pop of bright green to contrast the creamy, warm pasta. Sometimes I’ll add a sprinkle of toasted pine nuts for a little crunch and extra depth, but even just the basil alone works wonders for color and flavor.

Side Dishes

I like pairing this recipe with a simple arugula salad tossed with lemon vinaigrette to cut through the richness. Garlic bread on the side is also a classic win, perfect for scooping up any leftover sauce on your plate.

Creative Ways to Present

For special occasions, I sometimes serve the shells family-style on a large wooden board, garnished with basil and little bowls of extra pesto. It creates a beautiful centerpiece and encourages sharing. You can also bake individual portions in small ramekins for a charming, personalized presentation.

Make Ahead and Storage

Storing Leftovers

Leftovers store wonderfully in an airtight container in the fridge for up to 3 days. I usually cover the baking dish tightly with foil or plastic wrap, then reheat individual portions as needed. The flavors actually meld even more after sitting, which I love.

Freezing

I’ve had great success freezing the assembled, unbaked shells. Just cover the dish tightly with foil, freeze, then bake straight from frozen—add 10-15 minutes to the bake time. This is a lifesaver for preparing ahead of busy weeks or unexpected company.

Reheating

To reheat, I cover the shells with foil to keep moisture in and warm them at 350°F until heated through, about 15-20 minutes. Removing the foil in the last 5 minutes helps revive the cheese topping’s lovely golden color and slight crisp.

FAQs

Can I make the Pumpkin Pesto Cheese Stuffed Shells Recipe vegetarian?

Absolutely! You can simply skip the chicken sausage and add extra veggies like sautéed mushrooms, spinach, or zucchini for a hearty filling. The pumpkin and cheeses provide plenty of savory flavor, so the dish stays satisfying without meat.
What can I substitute for pumpkin puree?

Butternut squash puree is a fantastic alternative that offers a similar creamy texture and mild sweetness. You can roast and puree your own fresh squash for an even fresher flavor, or use canned butternut squash puree if you’re short on time.
Can I prepare this dish ahead of time?

Yes! You can assemble everything up to the baking step, cover it, and refrigerate for up to 24 hours before baking. It’s great for meal prepping or hosting when you want to get dinner ready in advance.
What pesto should I use for the best flavor?

I recommend using fresh homemade basil pesto if possible—it’s more vibrant and aromatic than store-bought. But a high-quality jarred pesto will work fine too. Just choose one that’s bright green and fresh-tasting for the best results.

Final Thoughts

This Pumpkin Pesto Cheese Stuffed Shells Recipe has become one of my go-to dishes whenever I want comfort food with a little twist. It’s like the perfect hug on a plate—warm, creamy, and full of surprising flavor. I truly hope you give it a try and enjoy making it as much as I love sharing it. Trust me, once you do, it’ll become a favorite in your rotation too!