Name: Twice-Baked Honeynut Squash with Pecan Topping 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 truly heartwarming about a dish that’s creamy, crunchy, and bursting with fall flavors all at once. That’s exactly why I adore this Twice-Baked Honeynut Squash with Pecan Topping Recipe—every bite feels like a cozy hug, and it’s bound to be a star on your holiday table or anytime you want to impress with minimal fuss.

This image shows five halves of roasted butternut squash placed closely on a white plate with blue floral patterns, set on a white marbled surface. Each squash half has a bright orange, soft interior filled with a crunchy topping of golden-brown crumbs and small chopped nuts, scattered evenly over the surface. Thin sage leaves, dark green and slightly crisp, are laid on top of the crumb topping, adding texture and color contrast. The light reflects warmly on the squash, highlighting their caramelized edges, while a glass of amber liquid appears in the background. 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 Pecan Topping Recipe
Top Tip
How to Serve Twice-Baked Honeynut Squash with Pecan Topping Recipe
Make Ahead and Storage
Frequently Asked Questions:
Final Thoughts
Twice-Baked Honeynut Squash with Pecan Topping Recipe

Why You'll Love This Recipe

I first made this twice-baked honeynut squash on a crisp autumn weekend, thinking it’d be a fun twist on regular stuffed squash. What blew me away was how the combination of sweet maple, savory sage, and crunchy pecans elevated the naturally nutty squash into something absolutely crave-worthy.

Perfect balance of flavors: Sweet, savory, and nutty come together in a way that’s sophisticated yet comforting.
Textural delight: The creamy squash filling contrasts beautifully with the crunchy pecan and panko topping.
Impress without stress: It looks fancy but is actually super simple to pull together—great for holiday guests or weeknight dinners.
Versatile side dish: Pairs wonderfully with almost anything from roasted turkey to a hearty grain salad.

The image shows a close-up of a butternut squash half filled with a textured orange mashed layer, topped with a crumbly golden-brown layer mixed with small chopped nuts and fresh sage leaves. The squash has a light orange skin and is placed on a white plate with blue floral patterns. A gold spoon is scooping some of the mashed filling, revealing the soft and creamy inside. The background is a white marbled texture. photo taken with an iphone --ar 2:3 --v 7

Ingredients & Why They Work

This recipe leans on the natural sweetness of honeynut squash and boosts it with layers of buttery, herbal, and nutty flavors. Each ingredient brings something special, and knowing why helps you nail the final taste.

Flat lay of three whole fresh honeynut squashes with bright orange skin and greenish tips, a small white ceramic bowl filled with extra-virgin olive oil, a few coarse grains of kosher salt and some black peppercorns scattered neatly, a small pat of pale yellow butter on a white ceramic dish, a white bowl with thinly sliced shallots displaying their purple and white layers, one whole uncracked brown garlic clove, a small pile of finely chopped fresh sage leaves with vibrant green color, a small white bowl containing smooth, creamy off-white crème fraîche, a small white bowl with amber-colored maple syrup, a small white bowl filled with finely grated pale yellow Parmesan cheese, a small white bowl with chopped light brown pecans, a small white bowl containing golden panko breadcrumbs, all ingredients arranged symmetrically and balanced, placed 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: Its smaller size and concentrated sweetness make it ideal for stuffing—plus, its tender flesh blends perfectly.
Extra-virgin olive oil: Adds richness and helps develop that golden crust on the topping.
Kosher salt and black pepper: Basic seasoning that enhances all the bright and earthy flavors.
Butter: Key for caramelizing the shallots, bringing deep savoriness to the filling.
Shallots: Their sweetness when caramelized pairs beautifully with the squash’s earthiness.
Garlic: A fragrant punch that lifts the entire dish.
Fresh sage leaves: There's something magical about sage with squash—it adds an aromatic woodsy note.
Crème fraîche (or softened cream cheese): Makes the filling luxuriously creamy and a bit tangy without overpowering.
Maple syrup: Ties into the autumn vibe with subtle sweetness and depth.
Parmesan cheese: Provides savory sharpness and helps the topping brown gorgeously.
Pecans: Offer crunch and nutty richness that contrasts the softness underneath.
Panko breadcrumbs: Light and crisp, perfect for a crunchy topping.

📝

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

One of the reasons I keep coming back to this Twice-Baked Honeynut Squash with Pecan Topping Recipe is how well it adapts to different tastes. I’ve played around with it a lot, so here’s how you can tweak it to suit your kitchen style.

Variation: I sometimes swap the sage for thyme or rosemary depending on what I have on hand; it changes the herbal note but keeps that cozy vibe going strong.
Dietary tweak: To make it vegan, substitute butter with a plant-based spread and crème fraîche with coconut cream—though the flavor will shift, it’s still delicious.
Option for extra texture: Try adding dried cranberries or chopped apples into the filling for a touch of tart sweetness.

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

Step 1: Roast the Honeynut Squash to Tender Perfection

First things first: preheat your oven to 425ºF. Slice your honeynut squashes lengthwise and scoop out the seeds—the fresh aroma hitting your kitchen this early on reminds me of fall’s bounty. Lay the squash halves cut side down on a baking sheet, drizzle them with half the olive oil, and sprinkle with kosher salt and pepper. Roasting with the cut side down locks in moisture, making the flesh tender and sweet. After about 20-25 minutes, poke them gently with a fork; they should be fork-tender but not mushy. Timing varies depending on squash size, so keep an eye close.

Step 2: Caramelize Shallots with Garlic and Sage

While the squash roasts, melt butter in a medium skillet over medium heat. I like to watch closely and turn down the heat to medium-low after a few minutes—it allows the shallots to caramelize slowly, drawing out their natural sweetness without burning. After about 6-7 minutes, they’ll look golden and fragrant. Then, toss in the minced garlic and fresh sage, cooking just another 1-2 minutes. The kitchen smells amazing at this point, trust me! Season lightly with salt, then remove from heat to keep the flavors fresh.

Step 3: Blend and Fill the Squash Boats

Once the squash is cool enough to handle, scoop out most of the flesh, leaving about a ¼-inch border intact to hold the filling. Pop the scooped squash into a food processor along with crème fraîche, maple syrup, and half of the Parmesan cheese. Blend until smooth and luscious. Next, add the caramelized shallot mixture and pulse a few times just to combine everything evenly. Spoon this creamy mix back into your squash boats—fill them about two-thirds full; if you want more filling, I suggest only filling 5 halves if you started with 3 squashes to avoid overstuffing.

Step 4: Assemble the Pecan-Panko Topping

In a small bowl, mix chopped pecans, panko breadcrumbs, remaining Parmesan, and the rest of the olive oil with a pinch of salt. This combo creates the perfect crunchy crust. For an extra touch I love, rub leftover sage leaves in olive oil and scatter over the topping. This not only adds crunch but also a gorgeous crispy herb flavor. Arrange the topping evenly on each filled squash half.

Step 5: Final Bake Until Golden and Crisp

Return the squash boats to the oven and bake for about 15 minutes. What you’re looking for is bubbly warmth beneath and a golden, crisp crust on top. When it comes out, the contrast of creamy squash and crunchy pecans will have you hooked. Let them cool briefly if you like, then dig in.

Top Tip

After making this Twice-Baked Honeynut Squash with Pecan Topping Recipe multiple times, I picked up a few tricks that made all the difference. Here’s what helps me get it right every time, and I’m sure they’ll help you too!

Don’t over-roast the squash: Keep an eye around 20 minutes and test with a fork—it should be tender but not collapsing, to hold its shape for stuffing.
Slow caramelization is key: Medium-low heat for shallots prevents bitterness and brings out that natural sweetness that balances the dish.
Sage goes in two ways: Fresh chopped in the filling and whole leaves rubbed in oil for crisp garnish adds layered herbal brightness.
Use panko for topping: The lightness is essential for a crispy topping—don’t swap it out for regular breadcrumbs unless you want a denser crust.

How to Serve Twice-Baked Honeynut Squash with Pecan Topping Recipe

Garnishes

I love topping these squash boats with a little extra fresh sage sprinkled right as they come out of the oven—it adds a fresh aroma and a pop of color. Sometimes, I drizzle a touch more maple syrup if I’m craving an added sweetness contrast to the savory notes.

Side Dishes

To round out the meal, I often serve this with roasted turkey or chicken, sautéed greens like kale or spinach, and a simple wild rice pilaf. It’s rich and comforting, so pairing it with lighter sides helps keep everything balanced.

Creative Ways to Present

For special occasions, I’ve arranged these squash halves on a large wooden board with a scattering of roasted nuts and fresh herbs all around—makes for a stunning centerpiece. You can also add edible flowers or a drizzle of browned butter sauce for a luxurious touch that always wowed my guests.

Make Ahead and Storage

Storing Leftovers

I usually cool leftovers completely, then cover tightly with plastic wrap or store in an airtight container. They keep well in the fridge for up to 3 days. The topping softens a bit in storage, but reheating crisps it back nicely.

Freezing

I’ve frozen filled but unbaked squash halves wrapped tightly in foil and placed in a freezer-safe bag. When I’m ready, I thaw them overnight in the fridge and then bake straight from chilled—adding a few extra minutes to the bake time. The texture and flavor remain excellent!

Reheating

Reheat in a 350ºF oven for 10-15 minutes until warmed through and the topping regains its crunch. Microwaving works in a pinch but tends to make the topping soggy, so I reserve that for busy days.

Frequently Asked Questions:

Can I make Twice-Baked Honeynut Squash with Pecan Topping Recipe ahead of time?

Absolutely! You can prepare it up to the step where you add the pecan topping and refrigerate it for a day before baking. Just add a few extra minutes to the final bake so it heats through completely.

What if I can’t find honeynut squash?

Butternut squash is a great substitute. Just note that honeynut squash is smaller and sweeter, so adjust roasting time accordingly—larger squashes might take longer to become tender.

Can this recipe be made vegan?

Yes! Swap butter for vegan margarine or coconut oil, and substitute crème fraîche with a full-fat coconut cream or a vegan cream cheese alternative. The flavor will shift slightly but still be delicious.

How do I make sure the pecan topping stays crunchy?

Use panko breadcrumbs instead of regular breadcrumbs, and bake the squash uncovered so the topping can crisp up. Adding a little oil and Parmesan to the topping also helps it brown beautifully.

Final Thoughts

This Twice-Baked Honeynut Squash with Pecan Topping Recipe is genuinely one of my favorite dishes to pull out when I want to wow friends or family without spending all day in the kitchen. It’s approachable, packed with seasonal flavors, and the perfect blend of creamy and crunchy. Seriously, once you try it, you’ll find yourself coming back to it again and again—just like I do. Give it a go and let me know how it becomes your fall or holiday favorite too!