How To Make Stuffed Shells with Butternut Squash

baking dish with stuffed shells filled with butternut squash

I'm always trying to think of those fantastic holiday dishes that everyone can eat and everyone will love. My take on this classic stuffed shells dish uses butternut squash and a creamy cauliflower puree that bring the autumn harvest right to the table. Perfect as a side to compliment any holiday meal- but hearty enough to serve on it's own. I love that dish is so much lighter than the classic Italian cheese

The Trick to Butternut Squash For Filling

Butternut squash got its name because of its buttery texture and nutty flavor. It comes to its peak at the beginning of October, but can last for many weeks in a cool, dark place making it a great go-to vegetable. Always look for squash that has a hard skin with no dents or cuts.

When I make this butternut squash filling, I try to cut the squash in 2-inch pieces so that it roasts evenly. Sometimes, you can find pre-cut squash in the grocery store (this is what I use in the video). Roasting the squash ensures that all of the flavor gets sealed in and intensifies. In this recipe, I roast the squash with garlic and herbs, but you can improvise with spice mixes like this easy Magic Masala Spice Mix for a different kind of flavor profile. Wrap the squash pieces in foil to seal in moisture and flavor. Bake and Puree.

butternut squash in foil for cooking
butternut squash puree in a bowl

How To Make Stuffed Shells with Butternut Squash

  • Make the Butternut Squash Filling: You can make this up to 3 days in advance to save on time. Divide the squash between 2 squares of aluminum foil. Toss with the salt, oil, herbs, and garlic. Wrap and bake. Once tender, place in the food processor for a smooth puree.
  • Make the Creamy Cauliflower Puree: This saucey puree can also be made in advance (1 day ahead) or at the last minute. Place the cauliflower into a baking dish and you will set the shells inside after stuffing.
  • Cook The Shells: Place the shells in boiling water and cook for approximately 10 minutes until slightly more than al dente (follow package instructions). Drain and rinse with cold water to stop the cooking process.
  • Stuff The Shells: Stuff each shell with the squash mixture and set them, side by side, into the cauliflower puree in the baking dish. Top with Marinated Feta Cheese for some extra indulgence (optional). Cover with aluminum foil.
  • Get Ready To Serve: Preheat your oven to 375f. Set the baking dish in the center of the middle rack. Bake for 30-40 minutes until warmed through.
  • Top With Your Favorite Topping.
stuffed shells with butternut squash on a plate

What To Serve with Stuffed Shells

Squash is a wonderful canvas for a fall or winter meal. These stuffed shells can be served as is for a warm and comforting meal. Because the purees are so soft, I often like to add something crunchy for texture. Try dressing it up with a few of these fun and delicious fall accents:

  • My favorite Hazelnut Chimichurri recipe goes great with this- or even try mixing it up like I did in the video and substitute candied pecans for the hazelnuts.
  • Pomegranate Seeds
  • Spicy Greens like the Arugula I use in my video
  • Diced Apples in Lemon and Olive Oil


stuffed shells with butternut squash

Stuffed Shells with Butternut Squash

My take on this classic stuffed shells dish uses butternut squash and a velvety cauliflower puree that bring the autumn harvest right to the table. Perfect as a side dish to compliment any holiday meal- but hearty enough to serve on it's own. 
5 from 2 votes
Prep Time 15 minutes
Cook Time 1 hour 15 minutes
Course Recipes- Holidays
Cuisine American
Servings 8 serves 8
Calories 172 kcal


To Make the Squash Puree

  • 24 oz Diced Butternut Squash 2-inch dice (about 1 small squash)
  • 4 cloves Garlic sliced
  • ½ teaspoon Kosher Salt or to taste
  • 2 sprigs Fresh Rosemary
  • 1 tablespoon Grapeseed or Olive Oil

To Make the Stuffed Shells


  • Prepare your squash and cauliflower first.  Preheat the oven to 375f.  Set a large pot of water on the stove to boil.
  • If you are using a whole squash, cut off the ends and peel with a peeler.  Next, cut in half and remove all the seeds with a spoon.  Lay the squash flat side down and cut into approximate 2-inch pieces.  It does not need to be perfect because it will be puréed.
  • Tear off 2 squares of aluminum foil approximately 10-inches big.  Divide the squash, sliced garlic, salt, and rosemary between the 2 foils.  Drizzle with the oil and mix up lightly with your hands.  Fold the foil closed over the top by folding all the corners up towards the center and then folding in the corners to seal.
  • Bake the squash packets for 45-60 minutes until very tender when poked with a fork.
  • While the squash is baking, you can start your cauliflower in the boiling water.  Follow the recipe for it here.
  • Once the squash is done, transfer it to a food processor and puree for 1-2 minutes until smooth.  Remove and set aside until ready to use.  You should now have a butternut squash puree and a creamy cauliflower puree ready to go.  If you would like, you can get ahead on the recipe up until here and refrigerate the purees until ready to use.   When ready to complete, continue ahead.
  • Place a large pot of water on the stove and bring to a boil.  There should be plenty of room for the pasta to expand.  Once the water is boiling, gently place your pasta shells in the water.  Stir gently to make sure they don't stick.  Let cook for approximately 10 minutes, or follow instructions on packaging.  You want the shells to be cooked just slightly more than al dente.
  • When the pasta is cooked, drain into a colander and immediately rinse with cold water to stop the cooking process.
  • In a baking dish, spread the cauliflower puree so that it covers the bottom.
  • Take each shell and open up with one hand, while gently spooning butternut squash puree into the inside.  The filling will be very soft, so don't overfill.  This may take some practice, but that is part of the fun!  Place the stuffed shell in the baking dish on top of the cauliflower puree.  
  • Continue until all of the shells are stuffed and in the dish.  Crumble marinated feta over the top if you are using.  Cover with foil and bake for 30-45 minutes (depending if you are starting with warm filling or not).
  • Top with garnishes like Hazelnut Chimichurri, fried sage, or fresh greens and serve immediately.



This dish is a fantastic idea for a side dish at Thanksgiving.  All of the flavors we love at the holidays, with a unique spin that will be sure to be a hit.  Pin the recipe and bring to your next pot luck!


Serving: 1gCalories: 172kcalCarbohydrates: 27gProtein: 5gFat: 6gSaturated Fat: 1gPolyunsaturated Fat: 2gMonounsaturated Fat: 2gTrans Fat: 0.03gSodium: 1100mgPotassium: 542mgFiber: 4gSugar: 4gVitamin A: 9249IUVitamin C: 53mgCalcium: 78mgIron: 2mg
Keyword holiday recipes, plant based, stuffed shells, vegan, vegan holiday recipes, vegan holidays, vegan recipes
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