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The creamy butternut filling for these butternut squash stuffed shells is lightened up with a secret ingredient.  Plus, brown butter alfredo sauce!  Need I say more?

Butternut Squash Stuffed Shells in a baking dish

It’s the middle of October, and I am ready for the fall season. I’m ready to feel a chill in the air, ready to wear boots and sweaters, ready to spend afternoons snuggling in and drinking hot cocoa with the kids.

I’ve been craving soup and this weekend it was finally cool enough that I made one of our favorite roasted butternut squash soup recipes.  Our other favorite is this winter soup, full of squash, potatoes, and leeks. 

We’ve been getting lots of squash in our farm box, and I’ve had to get creative with how to use it like my butternut squash lasagna. Sometimes I’ll just toss cubes of squash with some olive oil, salt, and pepper, and we will have roasted butternut squash as a side dish. 

My family loves my spinach and cheese stuffed shells recipe so much that I thought I’d try butternut squash stuffed shells for a change.

pasta shells stuff with butternut squash in white rectangular baking dish

This butternut squash recipe is another favorite way to enjoy butternut squash. In this recipe, cottage cheese is a shortcut that blends in with the squash, adds some creaminess, and I find that I hardly know it’s there when I’m eating these shells. If cottage cheese is just not your thing, go ahead and substitute ricotta.

How to Make Butternut Squash Stuffed Shells

Prepping these Butternut Squash Stuffed Shells involves a few steps, but they are all relatively simple. First, you’ll want to peel and chop your butternut squash into half-inch cubes. 

You’ll place the chopped squash in a baking dish, toss it with some olive oil, garlic, and Italian seasoning, and roast it in your oven at 425 degrees F until tender.

close up of a butternut squash stuffed shell on wooden spoon with baking dish in background

While the squash roasts, boil the jumbo shells and make the brown butter alfredo sauce. This creamy sauce starts with brown butter and fresh sage, and ends with Parmesan cheese and a dash of nutmeg. It’s a delicious complement to the creamy mashed butternut squash. You’ll mix some of the sauce into the mashed squash and pour the rest on top of the shells before baking.

Stuffing the squash/cottage cheese/alfredo mixture into the shells is really fast and easy. I like to sprinkle chopped walnuts on my shells before baking. The walnuts toast up as the shells bake and add another dimension of flavor and texture to the finished dish.

Brown butter, roasted squash, cheese, toasty walnuts… these Butternut Squash Stuffed Shells have so much deliciousness going on. They are a comforting fall meal that you’ll want to sit down to many times this season.

five butternut squash shells arranged on a white plate ready to eat

More Delicious Squash Recipes:


Butternut Squash Stuffed Shells in a white baking dish.

Butternut Squash Stuffed Shells

Servings: 6 servings
Prep Time: 35 minutes
Cook Time: 40 minutes
Total Time: 1 hour 15 minutes
The creamy butternut filling for these stuffed pasta shells is lightened up with a secret ingredient. Plus, brown butter alfredo sauce! Need I say more?


For the Stuffed Shells:

  • 1 medium butternut squash
  • 1 tablespoon olive oil
  • 2 cloves garlic, minced
  • ½ teaspoon Italian seasoning
  • salt and pepper
  • 24 jumbo pasta shells
  • 1 cup cottage cheese, or ricotta cheese
  • ½ cup chopped walnuts

For the Brown Butter Sage Alfredo Sauce

  • 3 tablespoons unsalted butter
  • 2 tablespoons chopped fresh sage
  • 2 cloves garlic, minced
  • 1 tablespoon all-purpose flour
  • 1 ½ cups lowfat milk
  • 1 cup grated Parmesan cheese
  • pinch of ground nutmeg
  • salt and pepper


Roast the squash:

  • Preheat oven to 425 degrees F. Peel, seed, and chop the butternut squash into ½-inch pieces. Place on a rimmed baking sheet and toss with the olive oil, garlic, Italian seasoning, ½ teaspoon salt, and a few grinds of black pepper. Roast in the oven for 25 minutes, until tender, stirring halfway through. Remove from the oven and lower oven temperature to 350 degrees F.

Cook the pasta shells:

  • Meanwhile, bring a large pot of salted water to a boil. Add the pasta shells and cook according to package directions for al dente, about 12 minutes. Drain and lay shells on a sheet of parchment paper to cool.

While the squash and pasta cook, prepare the brown butter alfredo sauce:

  • In a medium saucepan, melt the butter over medium-low heat. Add the sage and continue to cook, stirring constantly, until brown flecks appear in the butter. Be very careful as the butter can go from brown to burned very quickly. Remove the pan from the heat and add the garlic. Slowly whisk in the flour; return the pan to the heat and whisk in the milk. Cook, stirring, until sauce thickens. Remove from the heat and stir in the Parmesan, nutmeg, and salt and pepper to taste.

Fill the shells:

  • Scoop the roasted squash into a medium bowl. Use a fork to mash the squash. Add the cottage cheese and ½ cup of the alfredo sauce and stir to combine.
  • Spray a 9x13-inch baking dish with cooking spray. Scoop about 1 ½ tablespoons of the squash mixture into each shell and place shells, seam side up, in the baking dish. Pour the remaining alfredo sauce over the shells. Sprinkle with the chopped walnuts. Bake, uncovered, for 12-15 minutes until hot. Serve.
Serving: 4stuffed shells, Calories: 451kcal, Carbohydrates: 47g, Protein: 20g, Fat: 22g, Saturated Fat: 9g, Cholesterol: 39mg, Sodium: 417mg, Potassium: 709mg, Fiber: 4g, Sugar: 8g, Vitamin A: 13771IU, Vitamin C: 27mg, Calcium: 385mg, Iron: 2mg
Nutrition information is an estimate.
Cuisine: Italian
Course: Main Dish, Pasta
Tried this recipe?Mention @kristines_kitchen on Instagram or tag #kristineskitchenblog.
Butternut Squash Stuffed Shells with Brown Butter Alfredo Sauce - plenty of cheese, creamy squash, and BROWN BUTTER! Yum! Vegetarian. Pasta.
Butternut Squash Stuffed Shells with Brown Butter Alfredo Sauce - plenty of cheese, creamy squash, and BROWN BUTTER! Yum! Vegetarian. Pasta.
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