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 utterly comforting about the warm, rich flavors of squash baked to perfection. This Twice-Baked Honeynut Squash with Pecan Topping Recipe is a delightful twist on traditional sides that brings creamy, sweet, and crunchy textures together in one gorgeous dish. You’ll love how it fills your kitchen with an inviting aroma and makes every bite feel like a special occasion.

Five halves of roasted butternut squash are filled with a crumbly topping of chopped nuts and breadcrumbs, sprinkled with small green sage leaves. The squash flesh is bright orange and soft, framed by light brown skin edges. The white plate with a blue floral pattern holds the squash halves close together, some resting on fresh sage sprigs. The background shows a white marbled surface with a glass of amber liquid nearby. The 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 with Pecan Topping Recipe when I wanted something cozy and a little different for the holidays—and it quickly became one of my favorite sides to bring to any fall gathering. It's elegant, easy to make, and has that perfect balance of sweet, savory, and crunchy.

Creamy and Crunchy: The smooth, sweet squash filling topped with pecans and crispy breadcrumbs gives you a texture combo that’s hard to resist.
Simple Ingredients: It uses pantry staples and fresh sage for that aromatic flavor pop without complicated prep.
Seasonal Favorite: Perfect for cozy fall meals, Thanksgiving dinner, or impressing guests with a unique veggie side.
Make-Ahead Friendly: You can prep most steps in advance, making holiday cooking so much smoother.

The image shows two halves of roasted squash placed on a white plate with blue floral patterns, sitting on a white marbled surface. Each squash half has a deep orange, soft, and slightly mashed flesh base, topped with a crumbly golden layer of chopped nuts and breadcrumbs. There are also small green herb leaves scattered on top, adding a touch of color and texture. One squash half has a utensil scooping into the soft flesh, showing the creamy inside with some of the crunchy topping mixed in. Photo taken with an iphone --ar 2:3 --v 7

Ingredients & Why They Work

This recipe balances flavors and textures thoughtfully. The honeynut squash brings sweetness and creaminess, butter and shallots enrich the filling with silkiness and depth, while pecans and Panko add a satisfying crunch. Plus, fresh sage adds that wonderful herbal note that just screams fall.

Flat lay of three whole fresh honeynut squashes with smooth orange skin, a small mound of thinly sliced pale purple shallots on a simple white ceramic plate, one whole uncracked white garlic clove, a few finely chopped fresh green sage leaves scattered loosely on the surface, a small white ceramic bowl filled with glossy extra-virgin olive oil, another small white bowl holding soft white crème fraîche, a neat pile of golden brown panko breadcrumbs on a white plate, a small heap of finely chopped light brown pecans on a white ceramic dish, a crisp pat of pale yellow butter, a small white bowl with finely grated pale yellow Parmesan cheese, a small white bowl of pure white kosher salt crystals, and a few whole black peppercorns arranged symmetrically — all components fresh and natural, 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: A smaller, sweeter cousin of butternut squash with denser flesh perfect for stuffing.
Extra-Virgin Olive Oil: Used both for roasting and making the topping luscious and golden.
Kosher Salt and Black Pepper: Essential to season every layer and bring out natural flavors.
Butter: Adds richness and helps caramelize the shallots beautifully.
Shallots: Their mild sweetness melts into the filling perfectly.
Garlic: Provides a heady aroma without overpowering the squash.
Fresh Sage: The star herb here, giving an earthy, piney fragrance that complements the squash.
Crème Fraîche (or Softened Cream Cheese): Adds creaminess and a slight tang that balances the sweetness.
Maple Syrup: Enhances natural sweetness and ties the flavors together.
Parmesan Cheese: Brings umami and a salty kick to the filling and topping.
Chopped Pecans: For that delightful crunch and nutty richness.
Panko Breadcrumbs: Ensure the topping crisps up nicely in the oven.

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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

What I love most about this Twice-Baked Honeynut Squash with Pecan Topping Recipe is how flexible it is. Feel free to swap in ingredients or tweak the topping to suit your taste and occasion.

Variation: I once swapped the pecans for walnuts when that’s what I had handy, and it was just as delicious—it brought a slightly earthier crunch that still worked beautifully.
Dairy-Free Option: Try using a vegan butter and a non-dairy cream cheese alternative to keep it creamy and plant-based.
Spicy Twist: Add a pinch of cayenne or smoked paprika to the pecan topping for a subtle heat contrast.
Herbs: Rosemary or thyme can be fun alternatives or additions to the fresh sage if you want to experiment.

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

Step 1: Roast the Honeynut Squash Just Right

Start by preheating your oven to 425ºF. Slice your honeynut squash in half lengthwise and scoop out those seeds—that’s always a satisfying little task for me. Place the halves cut side down on a rimmed baking sheet, drizzle with half the olive oil, then season with salt and pepper. Roasting them with the cut sides down traps the steam inside for tender, fork-ready flesh in just 20–25 minutes. Keep an eye on them around 20 minutes to avoid overcooking; you want tender but not mushy.

Step 2: Caramelize Shallots for That Layered Flavor

While the squash roasts, melt your butter in a skillet over medium heat and toss in the thinly sliced shallots. Cook gently, stirring often, until they're soft and golden—about 6 to 7 minutes. I usually turn the heat down a bit after a few minutes to prevent burning; patience here pays off big time. Then add the minced garlic and fresh sage, cooking for an extra 1–2 minutes until everything smells irresistible. Season lightly with kosher salt and remove from heat.

Step 3: Scoop and Blend the Filling

Once your roasted squash is cool enough to handle, carefully scoop out most of the flesh, leaving about a ¼-inch border so the "boats" hold their shape. Pop the scooped flesh into a food processor along with crème fraîche, maple syrup, and half the Parmesan. Blend until smooth, then add the caramelized shallots mixture and pulse just enough to combine everything nicely. This mixture is the creamy heart of the dish, and I love how the sweet and herbaceous notes come alive here.

Step 4: Fill and Top Your Squash Boats

Spoon the filling evenly back into the squash halves—this recipe makes about six halves (from three squashes), and I usually fill them about two-thirds full to leave room for the crunchy topping. In a small bowl, combine chopped pecans, Panko breadcrumbs, remaining Parmesan, olive oil, and a pinch of salt. Sprinkle this over the filled squash, then if you love crispy sage leaves as much as I do, rub the remaining leaves in olive oil and scatter them over the topping for a fragrant, golden finish.

Step 5: Bake Until Golden and Glorious

Pop your loaded squash back into the oven for about 15 minutes. You'll know they're ready when the filling is warmed through and the topping turns a beautiful golden brown with a satisfying crunch. I can’t tell you how many times the aroma alone made me sneak a taste before plating! Serve warm and enjoy.

Top Tip

From my experience making this Twice-Baked Honeynut Squash with Pecan Topping Recipe, the key to getting that perfect balance of creamy filling and crisp topping lies in not overfilling the squash halves and taking your time caramelizing the shallots.

Caramelize Gently: Lower the heat after a few minutes when cooking shallots—this prevents burning and brings out their rich sweetness.
Don’t Skip the Sage: Fresh sage is a game-changer here—both in the filling and as a crispy garnish that adds a herby wow factor.
Use Panko: Panko breadcrumbs give that unbeatable crunch when baked; regular breadcrumbs just don’t compare.
Check Squash Doneness Early: Because honeynut size varies, start checking at 20 minutes to avoid overcooking the squash halves initially.

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

Garnishes

I like to finish these squash boats with a few extra toasted pecans or a sprinkle of fresh sage leaves if I’m serving guests. A light drizzle of good-quality maple syrup on top after baking adds a subtle shimmer and extra sweetness that some folks really enjoy.

Side Dishes

This Twice-Baked Honeynut Squash pairs wonderfully with roasted Brussels sprouts, a green salad with lemon vinaigrette, or even a creamy risotto for a comforting autumn meal. For Thanksgiving, it stands out alongside turkey and mashed potatoes.

Creative Ways to Present

For special occasions, try serving the squash boats on a long wooden board sprinkled with extra pecans and sage leaves scattered around for an inviting autumnal display. You can even scoop the filling into mini squash halves to create individual appetizers that wow guests!

Make Ahead and Storage

Storing Leftovers

I usually store leftover squash boats in an airtight container in the fridge for up to 3 days. They keep well, but the topping might soften a bit—re-crisping in the oven revives them nicely.

Freezing

If you want to freeze this Twice-Baked Honeynut Squash with Pecan Topping Recipe, I recommend freezing before adding the pecan topping. Wrap squash halves tightly in foil or plastic wrap, freeze for up to 2 months, then add topping and bake fresh when ready to serve.

Reheating

To reheat leftovers, pop them in a 350ºF oven for about 15 minutes, or until warmed through and the topping is crisp again. Avoid microwaving if you want to keep that perfect texture.

Frequently Asked Questions:

Can I use butternut squash instead of honeynut squash?

Absolutely! Butternut squash works as a great substitute. Just adjust the roasting time slightly since it’s larger and less dense than honeynut. Expect it to take a bit longer to become fork tender.

What can I use instead of crème fraîche?

You can swap crème fraîche with softened cream cheese for a similar creamy texture and tang. Greek yogurt might work too but may make the filling a bit looser, so reduce any added liquids accordingly.

How do I make this recipe vegan?

Use vegan butter or olive oil in place of regular butter, a non-dairy cream cheese alternative instead of crème fraîche, and skip the Parmesan or use a plant-based cheese substitute. Toast the pecans and Panko in olive oil to add richness.

Can I prepare the filling ahead of time?

Yes, you can prepare and blend the filling a day ahead and keep it covered in the refrigerator. When ready, spoon the filling into the squash boats and add the topping before baking. This speeds up assembly on the day you serve.

Final Thoughts

This Twice-Baked Honeynut Squash with Pecan Topping Recipe has become a little celebration of fall in my kitchen—a dish that always brings warmth and smiles around the table. I hope you try making it soon, and that it finds a happy spot in your seasonal cooking, just like it did in mine. Here’s to cozy meals and gatherings made better with simple, delicious food!