Stuffed Butternut Squash


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Stuffed butternut squash is filled with a satisfying combination of fluffy quinoa, toasted pecans, and savory garlic and thyme. This comforting vegetarian meal is topped with a cheesy, crunchy topping and is the perfect holiday side dish or weeknight dinner.

stuffed butternut squash halves on a white platter

There is something so comforting in the flavors of warm butternut squash. This fall and winter favorite becomes sweet and caramelized when you bake it, and the vibrant orange flesh turns fork-tender. Taking the extra step of twice-baking the squash gives this meal a bubbling hot top of melted cheese and crispy, golden-brown breadcrumbs.

What’s great about this recipe is there are dozens of ways to customize the squash stuffing. You can go totally vegetarian, or make it extra hearty by adding ingredients like sausage, mushrooms, or wild rice. No matter how you fill these squashes, the cheesy, herby, flavors make the best comforting weeknight meal, and will always please a crowd. 

How to Make It

  1. Prep the squash. Slice the squash lengthwise, and scoop out the seeds. Next, place the squash halves in a large baking dish and cover with ¼ inch of water.
  2. Bake the squash. Bake the squash for 30-50 minutes. The baking time will depend on the size of the squash.
  3. Cook the quinoa stuffing. While the squash bakes, cook the quinoa. Remove from heat and set aside when done.
  4. Saute the aromatics. In a skillet over medium heat, saute the shallots, garlic, pecans, and dried thyme. Cook, stirring often, about 5 minutes. Meanwhile, remove the squash from the oven and let cool.
  5. Make the stuffing mixture. Scrape the flesh out of the roasted squash, and mix that with the shallots and pecans. Mash everything together, and then add the cooked quinoa and salt.
  6. Stuff the squash. Spoon the filling into the prepared squash halves. Then, stir together the melted butter, panko breadcrumbs, and cheese, and press into the tops of the squash.
  7. Finish the squash in the oven. Return squash to the oven and bake until the crust is golden brown, 15 to 20 minutes.
scooping out butternut squash halves
baked squash halves in a white baking dish
toasting pecans in a cast iron skillet


  • Butternut Squash – Soft and tender butternut squash is the perfect canvas for building flavor. If butternut squash is unavailable, you can also use acorn squash.
  • Water – Helps to cook the squash and prevents sticking to the baking sheet.
  • Uncooked Quinoa – The base of the squash stuffing. 
  • Olive Oil, Shallots, Garlic, Pecans, Dried Thyme – The combination of aromatic shallots, minced garlic, crunchy pecans, and earthy thyme infuse the quinoa with flavor. 
  • Kosher Salt – Basic pantry ingredient to lift flavor.
  • Unsalted Butter – Unsalted butter allows you to control the salt content.  
  • Panko Breadcrumbs – Adding panko breadcrumbs to the stuffing mixture creates a satisfying filling, and helps to bind the other ingredients together.
  • Gruyere Cheese – A beautiful melting cheese from Switzerland that makes the best cheesy quinoa filling. 

Make ahead

You can make stuffed butternut squash a day ahead of time. After you stuff the squash, cover with foil, and refrigerate. When you’re ready to serve, let the squash come to room temperature, then finish in the oven at 400 degrees F for 15 to 20 minutes.

How to Store

Store stuffed butternut squash for 4 to 5 days in the refrigerator. You can also freeze this dish in a sealed container for up to 3 months. To reheat the squash, thaw in the refrigerator for 24 hours, then reheat in the oven at 350 degrees F for 20 to 30 minutes.

Recipe Tip

If using acorn squash in place of butternut squash, reduce the bake time to 30 minutes.

stirring filling in a metal mixing bowl


  • Vary the stuffing – Barley, wild rice, long-grain white rice, and brown rice can be used in place of quinoa. 
  • Add dried fruit – Dried fall fruits work great with savory squashes. Chop cranberries and sour cherries for a nice tart-sweet contrast to the squash.
  • Try different herbs and spices – Sage and rosemary are magical with squash. A touch of cinnamon, nutmeg, or ginger will create the perfect fall side dish. 
  • Swap cheeses – Parmesan, Asiago, or mozzarella can be used in place of Gruyere cheese.
  • Sneak in veggies – It’s so easy to add some leafy greens to this butternut squash stuffing. Chopped kale or spinach adds an extra nutritional boost to this vegetarian meal. 
  • Fill with protein – Speciality sausages like chicken and apple or caramelized onion make a delicious sausage stuffed squash. Or, top with crumbled pieces of crispy bacon.


Do you peel butternut squash before baking?

There’s no need to peel butternut squash before baking. Leaving the skin on the squash gives you the perfect shell to hold all of the delicious squash stuffing, and makes it easy to scoop out the flesh. 

How long does it take for butternut squash to soften in the oven?

The cook time for butternut squash depends on the size of the squash. A smaller squash will take 30 to 40 minutes, while a larger squash may need up to 50 minutes to become fork-tender.

topping butternut squash with breadcrumb mixture

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stuffed butternut squash on a white platter

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baked butternut squash on a white rectangular tray
5 from 1 vote

Stuffed Butternut Squash Recipe

Stuffed butternut squash is filled with a satisfying combination of fluffy quinoa, toasted pecans, and savory garlic and thyme. This comforting vegetarian meal is topped with a cheesy, crunchy topping and is the perfect holiday side dish or weeknight dinner.
Prep: 30 minutes
Cook: 1 hour
Total: 1 hour 30 minutes
Servings: 8


  • Baking Dish
  • Saucepan
  • Mixing Bowls
  • Nonstick Skillet


  • 3 pounds butternut squash (1 large or 2 small)
  • 2 tablespoons olive oil, divided
  • 1 1/2 cup low-sodium vegetable stock
  • 3/4 cup uncooked quinoa
  • 1/4 cup minced shallots
  • 2 cloves garlic, minced
  • 2/3 cup pecans, roughly chopped
  • 1 teaspoon dried thyme
  • 1 teaspoon Kosher salt
  • 1 teaspoon apple cider vinegar
  • 4 tablespoons unsalted butter
  • 3/4 cups panko breadcrumbs
  • 3 ounces gruyere cheese, finely grated
  • 2 tablespoons finely chopped parsley


  • Preheat the oven to 450 degrees F.
  • Slice the squash in half lengthwise and scoop out the seeds. Drizzle a large baking dish with 1 tablespoon of olive oil. Place the squash halves cut-side down in a large baking dish. Pierce the skin of the squash a few times with a knife.
  • Bake the squash until it is tender when pierced with a fork, 30-40 minutes, depending on size.
  • While the squash cooks, cook the quinoa by bringing the stock to boil in a small saucepan. Add the quinoa and stir once. Reduce the heat to low-medium and cover with a lid. Cook, covered for 15 minutes. Remove the pan from the heat.
  • Heat a large skillet over medium heat. Add 1 tablespoon of olive oil. When the oil begins to shimmer, add the shallots, garlic, pecans, and dried thyme. Cook, stirring often, until the shallots are very tender and the pecans are fragrant, about 5 minutes. Transfer the shallots and pecans to a large mixing bowl.
  • When the squash is done roasting, remove it from the oven and let it cool until you can safely hold it on a cutting board (using a clean dish towel to hold it in place helps).
  • Use a spoon or an ice cream scoop to scrape the flesh out of the roasted squash halves, leaving a layer of about 1/2 inch of squash remaining in the shell.
  • As you scoop out the squash, add it to the bowl with the shallots and pecans. Add the salt and vinegar. Mash everything together until even.
  • Add the quinoa to the mashed squash and gently fold it in.
  • Return the squash halves to the baking dish, cut-side up. Spoon the filling into the prepared squash halves.
  • Stir together the melted butter, panko breadcrumbs, and cheese. Press the panko crust into the tops of the squash.
  • Return squash to the oven and bake, uncovered, until the crust is golden brown, 15 to 20 minutes.
  • Sprinkle with parsley. Serve warm.


Calories: 318kcal | Carbohydrates: 38g | Protein: 9g | Fat: 17g | Saturated Fat: 6g | Polyunsaturated Fat: 3g | Monounsaturated Fat: 6g | Trans Fat: 0.2g | Cholesterol: 27mg | Sodium: 594mg | Potassium: 778mg | Fiber: 6g | Sugar: 5g | Vitamin A: 18547IU | Vitamin C: 38mg | Calcium: 222mg | Iron: 3mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Author: Jess Smith via Inquiring Chef
Cost: $8.00
Calories: 318
Keyword: butternut squash, easy vegetable side, fall recipe, holiday side dish, vegetable side dish, vegetarian
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About Jess Smith

Jess is the recipe creator and photographer at She spent nearly a decade as the Chief Recipe Developer for the award-winning meal planning app Cook Smarts. Her colorful, healthyish recipes have been featured in popular online publications including Parade, Hallmark, and HuffPost.

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  1. Made this but made a brown butter with sage and sauteed the onions in it. Left out the olive oil and oregano. It was AMAZING!! So perfectly delicious!!

    1. Christine – my husband was so excited that someone was requesting his favorite recipe of all time! I’ll definitely share it on the blog soon. They’re a classic in our house!

  2. This sounds absolutely amazing! Ever since my boyfriend and I started our backpacking trip in Asia I;ve seriously been missing quinoa and haven;t seen it anywhere! I’m guessing you were able to buy some in Bangkok?

    1. It took a little searching, but I have found quinoa in Bangkok, although I still always ask for it in care packages from home and plan to get red quinoa when I’m back in the U.S. over the holidays this month! A grocery store chain called Villa here in Bangkok sells all sorts of Bob’s Red Mill products – surprising, but definitely worth a splurge on occasion!

  3. This looks crazy good- I’ve never baked butternut squash like this, and it looks soooo good with the quinoa!

  4. I love baking butternut squash like this – stuffed and open-faced. I bet the quinoa adds such a nice pop of texture to it!

    1. This was my first time baking them like this, Averie, but I don’t know what took me so long! It’s a new favorite – so pretty and so easy!

  5. I think you segued nicely from the Prez to butternut squash. 🙂 I am stealing this stuffing recipe! It would make a great meal by itself.

    1. Debra – I was thinking the same thing. It’s festive, but it would be a good vegetarian meal all on its own. Looking forward to seeing what you’ve got cooking this week!

  6. Making a casserole with butternut, onions, cheddar for Thanksgiving. Totally not photogenic but yummm 🙂

    Moar Obama pls! – H from down the hall!

  7. Those squash are gorgeous and the filling looks right up my alley. Luckily, butternut is the one kind of squash that is actually really easy to find here. I’ll definitely be trying these out, thanks for the recipe!