This post contains affiliate links. As an Amazon Associate, I earn from qualifying purchases at no extra cost to you.
Jump to RecipeThese pumpkin pesto cheese stuffed shells are cozy fall comfort food at its best. Jumbo pasta shells are filled with a creamy mix of ricotta, fontina and basil pesto, nestled into a spicy pumpkin sauce with Italian chicken sausage and red bell pepper, then topped with torn mozzarella and baked until golden and bubbly. The sauce is savory, gently spiced and silky, and the herby cheese filling makes every shell irresistible.
It is a make ahead friendly casserole that is perfect for Sunday dinners, holiday gatherings or feeding a hungry family on a chilly night. Serve with a green salad and crusty bread. If you love stuffed pasta, try my easy spinach ricotta stuffed shells or Philly cheesesteak stuffed shells.
Why You Will Love These Stuffed Shells
- Perfect fall flavor. Pumpkin, sausage and warm spices make a cozy sauce.
- Three cheese filling. Ricotta, fontina and mozzarella with fresh pesto.
- Make ahead friendly. Assemble up to a day ahead and bake when ready.
- Feeds a crowd. A full pound of shells fills a 9×13 dish.
- Freezer friendly. Bake one now and freeze one for later.
Ingredients You Will Need
Here is what you need. Exact amounts are in the recipe card below.
For the spicy pumpkin sauce
- Extra virgin olive oil: for browning the sausage.
- Spicy Italian chicken sausage: removed from its casing. Pork sausage or turkey sausage also work.
- Red bell pepper: chopped, for sweetness and color.
- Pumpkin puree: use pure canned pumpkin, not pumpkin pie filling.
- Chicken broth and whole milk: create a smooth, creamy sauce.
- Dried oregano and crushed red pepper flakes: add herby flavor and a little heat.
- Kosher salt and black pepper.
For the cheese stuffing
- Jumbo pasta shells: the perfect vessel for stuffing.
- Whole milk ricotta cheese: creamy and slightly sweet.
- Shredded fontina cheese: melts beautifully and adds a nutty richness.
- Basil pesto: homemade or store bought, for fresh, herby flavor.
- Fresh mozzarella: torn, for a gooey golden top.
- Fresh basil: for garnish.
How to Make Pumpkin Pesto Stuffed Shells
1. Preheat the oven
Preheat the oven to 350°F and lightly grease a 9×13 baking dish.
2. Make the spicy pumpkin sauce
Heat the olive oil in a Dutch oven or large pot over medium high heat. Add the sausage and cook for 5 to 8 minutes, breaking it apart with a spatula, until browned and cooked through. Reduce the heat to low and stir in the red bell pepper, pumpkin puree, chicken broth, milk, oregano, red pepper flakes, salt and pepper. Simmer for about 15 minutes until slightly thickened. Taste and adjust the seasoning.
3. Cook the pasta shells
Meanwhile, bring a large pot of salted water to a boil. Cook the jumbo shells for 2 minutes less than the package directions, so they are pliable but still firm. Drain in a colander and rinse briefly with cool water so they are easy to handle. Spread them on a tray so they do not stick together.
4. Make the filling
In a mixing bowl, stir together the ricotta, fontina and pesto until well combined. Season with a pinch of salt and pepper.
5. Stuff and assemble
Spread about half of the pumpkin sauce in the bottom of the baking dish. Fill each shell with a heaping spoonful of the cheese mixture and arrange them in the dish, open side up. Spoon the remaining sauce over and around the shells and scatter the torn mozzarella over the top.
6. Bake
Cover with foil and bake for 20 minutes. Remove the foil and bake for another 10 to 15 minutes, until the cheese is melted, bubbly and lightly golden. Let rest for 5 minutes, then garnish with fresh basil and serve.
Tips for Perfect Stuffed Shells
- Undercook the shells slightly. They finish cooking in the oven and hold their shape better.
- Cook a few extra shells. Some always tear, so boil a handful more than you need.
- Use a piping bag. A zip top bag with the corner cut off makes filling fast and neat.
- Do not skip the foil. It keeps the shells moist while the filling heats through.
- Let it rest. A few minutes out of the oven helps the filling set.
Why Pumpkin Works in a Pasta Sauce
Pumpkin might seem like a dessert ingredient, but it makes a wonderful savory sauce. Pure pumpkin puree is naturally creamy and slightly sweet, with an earthy flavor that pairs beautifully with sausage, garlic, herbs and cheese. When simmered with milk and broth, it turns into a silky, velvety sauce that coats pasta like a cream sauce, but with fewer calories and more fiber and vitamin A. The spicy sausage and red pepper flakes balance the natural sweetness, and the oregano adds a classic Italian note. It is a simple way to bring fall flavor to a familiar baked pasta dish.
Pesto Tips and Substitutions
Pesto brings a fresh, herby flavor that brightens the rich cheeses. Store bought basil pesto is a great shortcut. Look for one made with olive oil and real Parmesan. If you prefer homemade, blend fresh basil, garlic, pine nuts, Parmesan, lemon juice and olive oil in a food processor. For a fall twist, try a kale or arugula pesto, or use sun dried tomato pesto for a richer, tangier filling. If you have a nut allergy in the family, choose a nut free pesto or make one with sunflower seeds.
Easy Variations
- Vegetarian: skip the sausage and add sautéed mushrooms and spinach to the sauce.
- Butternut squash: use butternut squash puree instead of pumpkin.
- Extra creamy: stir 2 ounces of cream cheese into the sauce.
- Spinach filling: fold a cup of chopped, well drained spinach into the ricotta.
- Milder version: use sweet Italian sausage and skip the red pepper flakes.
- Different cheese: swap fontina for provolone, Gruyère or more mozzarella.
How to Fill Jumbo Shells Quickly and Neatly
Filling 30 or more shells can feel slow, but a few tricks make it quick. First, cook the shells until just pliable, then rinse them in cool water and lay them out in a single layer on a lightly oiled sheet pan so they do not stick together. Spoon the ricotta, fontina and pesto filling into a large zip top bag, press out the air and snip about 3/4 inch off one corner. Hold each shell open with one hand and pipe the filling in with the other. This is faster than using a spoon and keeps your hands clean. If a shell tears, you can still fill it and place it seam side down in the dish. Aim for about 2 tablespoons of filling per shell so they are generous but not overflowing. Arrange them snugly in rows so they support each other as they bake.
Serving Stuffed Shells for the Holidays
This dish is a wonderful make ahead main for Thanksgiving week, Friendsgiving or a cozy December gathering. It can be assembled the day before, which frees up your oven and your time on the day. Bake it just before guests arrive, and it will stay warm on the table for up to 30 minutes if you tent it loosely with foil. For a crowd, double the recipe and bake two dishes on separate racks, rotating halfway through. A vegetarian version without the sausage is great to have alongside so everyone has an option. Garnish generously with fresh basil and a drizzle of pesto for a colorful presentation.
What to Serve With Stuffed Shells
These shells are hearty, so fresh and crisp sides are best. Try a simple arugula salad with lemon vinaigrette, roasted Brussels sprouts or green beans, or a Caesar salad. Warm garlic bread is always a hit for scooping up the pumpkin sauce. For a full Italian inspired dinner, start with a bowl of creamy chicken and gnocchi soup.
Make Ahead, Storage and Freezing
- Make ahead: assemble the dish, cover tightly and refrigerate for up to 24 hours. Add 10 minutes to the covered baking time.
- Refrigerator: store leftovers covered or in glass meal prep containers for up to 4 days.
- Freezer: freeze the unbaked, assembled dish wrapped in plastic and foil for up to 3 months. Thaw overnight in the fridge before baking.
- Reheating: warm individual portions in the microwave or cover the dish with foil and reheat at 350°F for 20 to 25 minutes.
Frequently Asked Questions
Can I use pumpkin pie filling?
No. Pumpkin pie filling is sweetened and spiced. Use pure pumpkin puree for the savory sauce.
Can I make stuffed shells without sausage?
Yes. Leave it out for a vegetarian version and add mushrooms or spinach for extra heartiness.
How do I keep the shells from tearing?
Cook them just until pliable, rinse with cool water and handle them gently. Cook a few extras just in case.
What cheese can I use instead of fontina?
Provolone, Gruyère, Havarti or extra mozzarella all melt well.
Can I freeze stuffed shells?
Yes. Freeze the assembled, unbaked dish for up to 3 months, then thaw and bake.
How many shells are in a pound?
About 30 to 36 jumbo shells, enough for a 9×13 dish.
Final Thoughts
Pumpkin pesto cheese stuffed shells combine everything you love about fall comfort food in one cheesy, bubbly casserole. The spicy pumpkin sausage sauce, creamy three cheese pesto filling and golden mozzarella topping make it a dish your family will request again and again. Make it ahead for busy nights or double it for a holiday crowd.
Nutrition Per Serving
| Nutrient | Amount |
|---|---|
| Calories | 590 kcal |
| Protein | 32 g |
| Carbohydrates | 52 g |
| Fat | 28 g |
| Saturated Fat | 14 g |
| Fiber | 3 g |
| Sugar | 7 g |
| Sodium | 780 mg |
Nutrition values are estimates calculated from standard ingredient data and will vary with the brands and exact amounts you use.
Pumpkin Pesto Cheese Stuffed Shells
Ingredients
Method
- Preheat the oven to 350°F and grease a 9×13 baking dish.
- Brown the sausage in olive oil for 5 to 8 minutes. Lower the heat and add the bell pepper, pumpkin, broth, milk, oregano, red pepper flakes, salt and pepper. Simmer 15 minutes.
- Cook the shells 2 minutes less than the package directions, drain and rinse with cool water.
- Mix the ricotta, fontina and pesto.
- Spread half the sauce in the dish, fill the shells and arrange them on top. Cover with the remaining sauce and mozzarella.
- Bake covered 20 minutes, then uncovered 10 to 15 minutes until bubbly. Rest 5 minutes and garnish with basil.
