Butternut Squash And Cheese-Stuffed Shells Recipe

We may receive a commission on purchases made from links.

While we miss all of the fresh, colorful fruits and vegetables of the warm summer months (we're looking at you, sweet heirloom tomatoes), we have to give credit to the harvests of the colder winter months. Squash, which comes in many shapes, types, and sizes, is the unsung hero of the winter, giving us dozens of warming recipes that highlight the vegetable's neverending versatility. Butternut squash, a creamy, slightly sweet orange squash best known for its use in creamy soups, is perhaps the season's star vegetable, as its mild flavor and versatile texture is a good base for almost any flavor pairing. Best of all, it can be pureed and used in sauces as an easy way to add body and depth.

This butternut squash and cheese-stuffed shells recipe, written with developer Michelle McGlinn, highlights the creamy, nutty flavor of butternut squash by first combining it with Italian sausage and then making it into a creamy, cheesy sauce. Paired with three different types of melty cheeses, a pinch of cayenne, and fresh sage, this stuffed shell recipe is perfectly rich and balanced with the savory flavors of fall and winter. 

Gather the ingredients for butternut squash and cheese-stuffed shells

You'll first need one medium-sized butternut squash. You'll need about 2 cups of pureed butternut squash after roasting, so if you aren't sure, opt for a slightly larger squash and save any leftovers for other recipes. From there, you'll need olive oil, salt, pepper, jumbo pasta shells, Italian sausage, fresh sage, butter, garlic, heavy cream, cayenne, cheddar, gouda, and Parmesan. We suggest buying blocks of cheese to grate fresh, which will melt more easily than pre-shredded cheese.

Step 1: Heat up the oven

Preheat the oven to 400 F.

Step 2: Prep the squash

Cut the squash in half and scoop out the seeds.

Step 3: Season the squash

Oil each squash half with 1 tablespoon oil and sprinkle with 1 teaspoon salt and pepper.

Step 4: Bake the squash until tender

Place the squash cut-side down on a foil-lined baking sheet. Bake until very tender and browned, 50 minutes.

Step 5: Remove the skins and add to a blender

Remove the squash from the oven and let cool to touch. Scoop the squash from the skin and place into a blender.

Step 6: Blend until smooth

Blend until smooth, about 10-15 seconds. Set the squash puree aside.

Step 7: Cook the pasta

In the meantime, cook the shells until just barely al dente, then carefully drain.

Step 8: Heat oil in a skillet

Heat 1 tablespoon oil in a skillet over medium heat.

Step 9: Crumble the sausage

Add sausage and crumble until browned, about 5 minutes.

Step 10: Remove the sausage and let cool

Remove the sausage and add to a large bowl to cool slightly.

Step 11: Crisp the sage

In the same skillet, add the 7 whole sage leaves. Cook until crispy, about 3-5 minutes. Remove and reserve.

Step 12: Melt the butter

Melt the butter in a clean skillet over medium heat.

Step 13: Cook the garlic

Add the garlic and cook until fragrant, about 1 minute.

Step 14: Whisk the sauce together

Add 1 cup squash puree, heavy cream, and cayenne and whisk to combine smoothly. Bring to a simmer and cook until thick, about 3 minutes.

Step 15: Remove sauce from heat and add cheeses

Remove from the heat and add ⅛ teaspoon salt and pepper and ½ cup cheddar. Stir until smooth.

Step 16: Spread sauce into a casserole dish

Spread ½ of the sauce into a casserole dish.

Step 17: Combine the filling ingredients

Combine the sausage, chopped sage, gouda, Parmesan, and ½ cup cheddar in a bowl with 1 cup butternut squash puree. Mix to combine.

Step 18: Stuff the shells

Stuff the shells with the mixture and nestle them into the casserole dish.

Step 19: Top with remaining sauce

Top with the remaining cream sauce.

Step 20: Adjust the oven temperature

Lower the oven's heat to 350 F.

Step 21: Cover and bake the shells

Cover and bake the shells for 30 minutes, then uncover and bake for 10 minutes longer.

Step 22: Top the stuffed shells with crispy sage

Top with crispy sage to serve.

What to serve with butternut squash and cheese-stuffed shells

Butternut Squash And Cheese-Stuffed Shells Recipe

No Ratings

These butternut squash and cheese-stuffed shells feature a rich, cheesy, creamy, sausage-infused filling.

Prep Time
15
minutes
Cook Time
1.67
hours
servings
4
Servings
butternut squash stuffed shell in a casserole dish
Total time: 1 hour, 55 minutes

Ingredients

  • 1 (2-pound) butternut squash
  • 2 tablespoons olive oil, divided
  • 1 teaspoon + ⅛ teaspoon salt, divided
  • 1 teaspoon + ⅛ teaspoon pepper, divided
  • 12 jumbo pasta shells
  • 1 pound mild Italian sausage
  • 10 sage leaves, divided, 3 finely chopped
  • 2 tablespoons butter
  • 2 cloves garlic, minced
  • 1 cup heavy whipping cream
  • ⅛ teaspoon cayenne
  • 1 cup shredded cheddar, divided
  • ½ cup shredded gouda
  • ½ cup grated Parmesan

Directions

  1. Preheat the oven to 400 F.
  2. Cut the squash in half and scoop out the seeds.
  3. Oil each squash half with 1 tablespoon oil and sprinkle with 1 teaspoon salt and pepper.
  4. Place the squash cut-side down on a foil-lined baking sheet. Bake until very tender and browned, 50 minutes.
  5. Remove the squash from the oven and let cool to touch. Scoop the squash from the skin and place into a blender.
  6. Blend until smooth, about 10-15 seconds. Set the squash puree aside.
  7. In the meantime, cook the shells until just barely al dente, then carefully drain.
  8. Heat 1 tablespoon oil in a skillet over medium heat.
  9. Add sausage and crumble until browned, about 5 minutes.
  10. Remove the sausage and add to a large bowl to cool slightly.
  11. In the same skillet, add the 7 whole sage leaves. Cook until crispy, about 3-5 minutes. Remove and reserve.
  12. Melt the butter in a clean skillet over medium heat.
  13. Add the garlic and cook until fragrant, about 1 minute.
  14. Add 1 cup squash puree, heavy cream, and cayenne and whisk to combine smoothly. Bring to a simmer and cook until thick, about 3 minutes.
  15. Remove from the heat and add ⅛ teaspoon salt and pepper and ½ cup cheddar. Stir until smooth.
  16. Spread ½ of the sauce into a casserole dish.
  17. Combine the sausage, chopped sage, gouda, Parmesan, and ½ cup cheddar in a bowl with 1 cup butternut squash puree. Mix to combine.
  18. Stuff the shells with the mixture and nestle them into the casserole dish.
  19. Top with the remaining cream sauce.
  20. Lower the oven's heat to 350 F.
  21. Cover and bake the shells for 30 minutes, then uncover and bake for 10 minutes longer.
  22. Top with crispy sage to serve.

Nutrition

Calories per Serving 1,160
Total Fat 80.6 g
Saturated Fat 38.8 g
Trans Fat 0.9 g
Cholesterol 216.7 mg
Total Carbohydrates 73.2 g
Dietary Fiber 7.2 g
Total Sugars 10.0 g
Sodium 1,232.1 mg
Protein 43.2 g
The information shown is Edamam’s estimate based on available ingredients and preparation. It should not be considered a substitute for a professional nutritionist’s advice.
Rate this recipe

Can I make these butternut squash stuffed shells vegetarian?

These butternut squash and cheese-stuffed shells can easily be made vegetarian by first omitting the sausage and replacing with kale, spinach, or chard, or swapping for chickpeas for a similar texture. You can also simply omit the sausage and make an extra-cheesy butternut squash stuffed shell. To do this, we recommend doubling the amount of filling (or adding 1 cup of ricotta) so that there is enough to stuff each of the 20 shells.

You can also save on ingredients by buying a larger butternut squash, dicing 1 ½ cups, and roasting the pieces for 10 minutes to soften before stuffing into the shells with the cheesy filling. This way, the shells have texture beyond the creamy cheese filling, but don't require doubling the amount of cheese used in the recipe. You can roast the diced butternut squash in the same oven as the whole squash halves, but remember to remove the diced pieces after 10 minutes so that they retain their shape and texture.

Can I make any part of this dish ahead?

Stuffed shells are an elegant and show-stopping entree, partially because they take so much time to prepare. While you can boil the pasta and cook the sausage while the squash roasts in the oven, you still have to blend the squash, combine the filling, stuff the shells, make the sauce, and bake the mixture altogether before being able to serve. Because this can be time consuming on any day of the week and especially so before hosting a dinner party or special occasion, we suggest breaking the prep into parts that can be done days in advance.

The squash can be cooked, pureed, and stored in the refrigerator for up to 5 days in advance, which already saves time in preparing the final dish. The recipe can then be started and finished in under an hour, beginning with cooking the pasta shells and putting together the sauce. You can also cook the pasta shells in advance, though we recommend assembling the dish fully instead of storing the pasta shells on their own, which can cause them to stick and harden. If making only the pasta shells in advance, rinse and drizzle with oil, then store in a single layer in a plastic bag to best avoid sticking and tearing. For the best results, assemble the entire casserole up to 24 hours in advance, cover with foil and store in the refrigerator, then remove and bake until warm and bubbly just before serving.

Read More Recipes

Recommended