Name: Twice-Baked Honeynut Squash with Pecans Recipe
Prep time: 25 min
Cook time: 35 min
Total time: 1 h
Cuisine: American
Ingredients: 3 lbs. honeynut squash (about 3 squashes); 4 Tbsp. extra-virgin olive oil, divided; Kosher salt and black pepper to taste; 2 Tbsp. butter; 1 cup thinly sliced shallots; 1 garlic clove, minced; 2 Tbsp. finely chopped fresh sage leaves (plus more for garnish, if desired); 1/4 cup crème fraîche (sub softened cream cheese); 2 Tbsp. maple syrup; 6 Tbsp. grated Parmesan cheese, divided; 1/2 cup finely chopped pecans; 1/3 cup Panko breadcrumbs

There’s something about the warm, nutty aroma and the creamy texture that makes this Twice-Baked Honeynut Squash with Pecans Recipe truly stand out. It’s like your favorite fall flavors got a cozy upgrade, perfect for sharing around the table or enjoying as a comforting solo treat.

The image shows five pieces of roasted butternut squash on a white plate with blue floral designs, placed on a white marbled surface. Each squash is cut in half lengthwise, with a smooth, bright orange flesh layer that looks soft and cooked. On top of the orange layer, there is a crumbly, light brown topping made of chopped nuts and breadcrumbs, creating a crunchy texture. Scattered across the topping are several green sage leaves, providing color contrast and an herbal touch. The plate is garnished with a few more fresh sage leaves on the side. A clear amber-colored drink in a glass is visible near the top right corner. The lighting highlights the rich colors and textures, giving a warm, inviting feel. Photo taken with an iphone --ar 2:3 --v 7

Jump to:

Why You'll Love This Recipe
Ingredients & Why They Work
Make It Your Way
Step-by-Step: How I Make Twice-Baked Honeynut Squash with Pecans Recipe
Top Tip
How to Serve Twice-Baked Honeynut Squash with Pecans Recipe
Make Ahead and Storage
Frequently Asked Questions:
Final Thoughts
Twice-Baked Honeynut Squash with Pecans Recipe

Why You'll Love This Recipe

I’ve made this Twice-Baked Honeynut Squash with Pecans Recipe countless times, and it never fails to impress. The balance of sweet, savory, and crunchy textures makes it feel both elegant and homey at once. Plus, it’s surprisingly easy to customize!

Comforting Flavor Boost: Roasting the honeynut squash brings out its natural sweetness that pairs perfectly with creamy, tangy crème fraîche and earthy sage.
Textural Contrast: The pecan and panko topping adds just the right crispness to contrast the soft, velvety squash filling.
Impressive Yet Simple: This dish looks fancy but comes together with straightforward steps—perfect for both weeknight dinners and special occasions.
Seasonal and Stylish: Honeynut squash—smaller and sweeter than butternut—makes for a charming individual serving vessel that’s a feast for the eyes as well as the palate.

The image shows a white plate with blue floral designs holding halved roasted squash filled with bright orange mashed squash. Each squash half is topped with a golden-brown crumbly mixture of nuts and breadcrumbs and scattered green sage leaves. The texture of the filling looks soft and creamy, while the topping is crunchy. A gold spoon is scooping into one of the squash halves, showing the thick, smooth inner layer beneath the crunchy topping. The background is a white marbled texture. Photo taken with an iphone --ar 2:3 --v 7

Ingredients & Why They Work

Each ingredient in this Twice-Baked Honeynut Squash with Pecans Recipe plays a key role in creating that perfect balance of flavor and texture. Using fresh, high-quality components really elevates the dish, and knowing a little about why they work together will help you feel confident in the kitchen.

Flat lay of whole fresh honeynut squashes with their rich orange flesh visible from one halved squash, a few whole shiny black peppercorns scattered beside a small mound of coarse kosher salt, a pat of creamy butter, a small pile of thinly sliced pale shallots, a single garlic clove unpeeled, fresh vibrant green sage leaves, a small white ceramic bowl with smooth whipped crème fraîche, a small white bowl of golden maple syrup, another white bowl filled with finely grated pale Parmesan cheese, a handful of chopped glossy pecans, a small bowl of light golden Panko breadcrumbs, and a small white bowl holding extra-virgin olive oil, all arranged symmetrically and balanced on a clean white marble surface, soft natural light, photo taken with an iPhone, professional food photography style, fresh ingredients, white ceramic bowls, no bottles, no duplicates, no utensils, no packaging --ar 2:3 --v 7 --p m7354615311229779997

Honeynut Squash: Smaller and sweeter than butternut, it roasts quickly and its delicate flavor makes the filling taste naturally rich and comforting.
Extra-Virgin Olive Oil: Adds fruity richness and helps crisp the topping and roast the squash evenly.
Kosher Salt and Black Pepper: Simple seasoning that enhances all the other flavors without overpowering.
Butter: For caramelizing the shallots and building that deep, savory base flavor.
Shallots: Their sweet, mild onion flavor caramelizes beautifully for an aromatic filling component.
Garlic: Just a little punch to add complexity and depth.
Fresh Sage Leaves: Earthy and slightly peppery, sage heightens fall flavors and pairs so well with squash and pecans.
Crème Fraîche (or Softened Cream Cheese): Adds creaminess and a subtle tang to balance the natural sweetness of the squash.
Maple Syrup: Enhances natural sweetness with a toasty depth that feels extra cozy.
Parmesan Cheese: Sharp and salty, it enriches the filling and helps create a golden, savory crust with the topping.
Chopped Pecans: Offer irresistible crunch and a buttery nutty flavor that complements the squash perfectly.
Panko Breadcrumbs: Light and airy, they give the topping a delicate crispness without getting heavy.

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Note: You'll find the complete list of ingredients, along with their exact measurements, in the printable recipe card at the bottom of this post.

Make It Your Way

This Twice-Baked Honeynut Squash with Pecans Recipe gives you a delicious base that you can easily tweak based on what you have in your pantry or personal flavor preferences.

Variation: I like swapping out pecans for toasted walnuts once in a while—they add a slightly earthier crunch that’s just wonderful.
Dairy-Free: Use coconut cream or cashew cream instead of crème fraîche to keep it creamy and rich without the dairy.
Herb Swap: Sometimes I use thyme or rosemary if I’m feeling adventurous, and the flavors still blend beautifully.
Add a Protein Boost: Stir in some cooked quinoa or crispy bacon bits for a heartier side dish or light main course.

Step-by-Step: How I Make Twice-Baked Honeynut Squash with Pecans Recipe

Step 1: Roast the Honeynut Squash to Sweet, Tender Perfection

First things first: preheat your oven to 425ºF. I slice the honeynut squash in half lengthwise and scoop out the seeds—that part always feels satisfying, like prepping a little edible boat. Drizzle the cut sides with 2 tablespoons of olive oil and sprinkle with salt and pepper. Then, flip them over so that the cut side is down. Roasting this way concentrates the sweetness and helps the flesh get super tender in about 20 to 25 minutes. Keep an eye on them—bigger squash might take a little longer, but you want them fork-tender without getting mushy.

Step 2: Caramelize the Shallots for That Mouthwatering Aroma

While the squash roasts, melt 2 tablespoons of butter in a skillet over medium heat. Toss in the thinly sliced shallots and cook slowly, stirring often. I usually turn the heat down to medium-low after a few minutes to prevent burning. After about 6 to 7 minutes, they should be golden and sweetly caramelized. Add the minced garlic and fresh sage, cooking for another 1 to 2 minutes until everything smells heavenly. Don’t forget a pinch of kosher salt here to bring out the flavors. Then, take the pan off the heat and set it aside.

Step 3: Blend the Filling and Stuff Your Squash Boats

Once the squash halves are cool enough to handle, scoop out the flesh carefully, leaving about a quarter-inch border so the skins keep their shape. The goal is to remove most of the squash to blend, but keep those little boats sturdy. Pop that scooped squash into a food processor along with the crème fraîche, maple syrup, and half the grated Parmesan cheese. Blend it until smooth and creamy. Then add the caramelized shallot mixture and pulse a few times just to mix it all in nicely. Spoon the filling evenly back into the squash halves—you want to fill them about two-thirds full unless you prefer extra stuffing (in which case, filling only five halves might do the trick if you started with three squashes).

Step 4: Mix and Add the Crunchy Pecan Topping

In a small bowl, stir together the chopped pecans, panko breadcrumbs, the remaining Parmesan, 2 tablespoons of olive oil, and a pinch of salt. Give it a good mix until everything is coated and ready to crisp up in the oven. If you’re a fan of that crispy sage leaf garnish like I am, brush the remaining fresh sage leaves in olive oil and scatter 1 or 2 on top of each squash boat. It’s a little touch that takes things to the next level.

Step 5: Bake Again Until Golden and Glorious

Pop the stuffed squash back in the oven at 425ºF and bake for about 15 minutes. You want the filling to be heated through and the topping to turn a gorgeous golden brown with just the right crispness. That contrast between creamy squash and crunchy pecan crust is the star of the show here.

Top Tip

Through trial and error, I’ve learned a few simple things that make this Twice-Baked Honeynut Squash with Pecans Recipe foolproof and extra special each time. These little tricks will save you from common pitfalls and help the flavors shine:

Roast Cut Side Down: This traps steam and softens the squash flesh perfectly without drying it out.
Low and Slow Caramelizing: Turning down the heat when cooking shallots keeps them from burning and brings out their natural sweetness.
Leave a Squash Border: Scooping out but leaving a ¼-inch edge helps the squash boats hold their shape when baking the second time.
Don't Overfill: Filling the boats about two-thirds full prevents spilling and ensures even heating.

How to Serve Twice-Baked Honeynut Squash with Pecans Recipe

Garnishes

I love to finish these with a few crispy sage leaves on top for an earthy crunch and pop of color. Sometimes I sprinkle a little extra grated Parmesan for a subtle savory hit. A small drizzle of high-quality maple syrup over the top just before serving adds a sweet shimmer that really delights the palate.

Side Dishes

This recipe pairs beautifully with roasted meats like turkey or pork loin, making it a fantastic holiday side. I also enjoy it alongside a fresh arugula salad tossed with lemon vinaigrette—helps balance the richness of the squash. For a vegetarian meal, serving with a grain salad or warm lentils creates a hearty, satisfying plate.

Creative Ways to Present

For a special occasion, I’ve arranged these squash boats on a rustic wooden board surrounded by roasted chestnuts and fresh herbs—it makes a stunning centerpiece. You could also hollow out smaller honeynuts for individual servings at a dinner party or carefully portion the filling into ramekins topped with the pecan crumb for a fancy presentation that everyone will rave about.

Make Ahead and Storage

Storing Leftovers

After enjoying your meal, let any leftovers cool completely. I wrap them tightly in plastic wrap or store in an airtight container and keep them in the fridge for up to 3 days. When you’re ready to reheat, a gentle warmed oven works best to keep the topping crisp.

Freezing

I’ve frozen the filling separately before, and it reheats well when thawed overnight and baked fresh with the topping added just before baking. Freezing the assembled boats with topping isn’t as good since the topping can lose its crispness, so I recommend freezing components.

Reheating

For reheating leftovers, I preheat the oven to 350ºF and place the squash boats on a baking sheet, loosely tented with foil to prevent over-browning. After about 15-20 minutes, I remove the foil to let the topping crisp back up. This method keeps the filling creamy and the pecans crunchy — just like fresh.

Frequently Asked Questions:

Can I use butternut squash instead of honeynut squash?

Absolutely! Butternut squash works well, but since it’s larger and less sweet, you might want to adjust roasting times and consider adding a little extra maple syrup to mimic honeynut’s natural sweetness.

What if I don’t have crème fraîche?

You can substitute crème fraîche with softened cream cheese or even plain Greek yogurt for a slightly tangy creaminess that complements the squash nicely. Just make sure to drain excess moisture if you choose yogurt.

How do I make this recipe vegan?

Replace butter with a plant-based oil like coconut or olive oil for caramelizing shallots. Use vegan cream cheese or cashew cream in place of crème fraîche, and swap Parmesan cheese with a vegan alternative or nutritional yeast for a cheesy flavor.

Can I prepare this recipe in advance for a holiday meal?

Yes! Prepare everything up to stuffing the squash boats and refrigerate them covered for up to 24 hours. Just add the pecan topping and bake when you’re ready to serve, giving you a stress-free way to enjoy fresh flavors on the day.

Final Thoughts

This Twice-Baked Honeynut Squash with Pecans Recipe holds a special place in my recipe repertoire—it’s the kind of dish that feels like a warm hug during chilly days. The combination of creamy texture, fragrant herbs, and crunchy topping always brings a smile to my face, and I’m confident you’ll enjoy making it as much as eating it. Trust me, once you try this, it’ll earn a permanent spot on your seasonal table. So go ahead, grab some honeynut squash, and treat yourself and your loved ones to this cozy, crowd-pleasing dish.