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 so comforting about bites of sweet, savory, and crunchy all wrapped into one dish. This Twice-Baked Honeynut Squash with Pecan Topping Recipe brings that magic to your table — creamy roasted squash blended with caramelized shallots and sage, then topped with a nutty, crunchy pecan-Panko crust. It's honestly a little slice of fall heaven that's easier to make than it looks.

Five halves of roasted orange butternut squash are placed on a white plate with blue flower patterns, each topped with a crumbly, light brown nut and breadcrumb mixture with some darker brown toasted bits and garnished with green sage leaves. The squash has a soft and slightly shiny texture with a few caramelized edges. The plate rests on a white marbled surface, with a few fresh sage leaves beside the squash and a glass of amber-colored liquid nearby. 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’ve made this twice-baked honeynut squash recipe more times than I can count, especially during the fall and winter holidays. It’s got this wonderful balance of sweet and savory, with just enough richness from the crème fraîche and butter. Plus, the pecan topping adds the perfect crunch that keeps everyone coming back for seconds.

Perfect balance of flavors: Sweet honeynut squash pairs beautifully with savory shallots, sage, and Parmesan for a cozy yet elegant side.
Crunchy pecan topping: Adds texture and a nutty flavor contrast that makes this dish irresistibly delicious.
Impressive but easy: Looks fancy but the steps are straightforward — something you can confidently bring to holiday dinners.
Flexible and customizable: You can easily swap ingredients or adjust the topping to make it your own culinary signature.

The dish shows two halves of roasted squash placed on a white plate with blue floral patterns, set on a white marbled surface. Each squash half is filled with a bright orange mashed squash layer that looks soft and creamy. On top, there is a crumbly topping made of light brown breadcrumbs mixed with small pieces of chopped nuts that add texture. Green sage leaves are scattered gently on the filling, adding a fresh touch. A gold spoon is scooping some orange filling from one half, showing the soft inside and crunchy top clearly. The lighting highlights the warm colors and textures, making it look inviting and rich. Photo taken with an iphone --ar 2:3 --v 7

Ingredients & Why They Work

The stars of this dish each play their part to make the flavor magic happen — from the caramelized shallots adding savoriness to the rich pecan topping for texture. I always look for the freshest honeynut squash I can find, since their natural sweetness really shines here.

Flat lay of three whole fresh honeynut squashes with rich orange skin, a small white ceramic bowl of golden extra-virgin olive oil, a small white ceramic bowl of coarse kosher salt, a small white ceramic bowl of whole black peppercorns, a few pats of pale yellow butter, a small white ceramic bowl filled with thinly sliced pale pink shallots, a single whole garlic bulb next to a small white ceramic bowl containing minced garlic, fresh green sage leaves loosely arranged, a small white ceramic bowl of creamy off-white crème fraîche, a small white ceramic bowl of amber maple syrup, a small white ceramic bowl of finely grated pale golden Parmesan cheese, a small white ceramic bowl of roughly chopped pecans with rich brown shells, and a small white ceramic bowl of light golden panko breadcrumbs, all perfectly arranged with balanced spacing and symmetry, 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: Smaller and sweeter than regular butternut, their rich, creamy flesh is perfect for roasting and filling.
Extra-Virgin Olive Oil: Adds fruitiness and helps crisp up the topping without overpowering the squash’s sweetness.
Butter: Essential for caramelizing shallots, adding depth, and that silky texture we all crave.
Shallots: Their mild onion flavor caramelizes beautifully, contributing subtle sweetness and complexity.
Garlic: Just a touch for warmth and aroma without overshadowing other flavors.
Fresh Sage: Earthy and aromatic — sage pairs perfectly with squash and nuts for an autumnal vibe.
Crème Fraîche (or softened cream cheese): Brings creamy tang and richness to the filling.
Maple Syrup: A touch of natural sweetness that complements the savory notes beautifully.
Parmesan Cheese: Adds umami depth and helps bind the filling and topping.
Pecans: Toasted for crunch and a buttery nuttiness that's the topping star.
Panko Breadcrumbs: Light and crispy, they create that lovely golden crust on top.
Kosher Salt & Pepper: To taste — don’t skip seasoning, it's key to pulling all the flavors together.

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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

I like to switch up the toppings sometimes, depending on what’s in my pantry or my mood. This recipe invites personalization — feel free to get creative and make it yours!

Variation: One time, I added a pinch of smoked paprika to the pecan topping for a subtle smoky warmth — it was delicious and added a fun twist.
Dairy-Free: Swap the crème fraîche for coconut cream and use vegan butter to make this recipe completely dairy-free without losing creaminess.
Nut-Free: Replace pecans with toasted sunflower seeds or pumpkin seeds for a safe alternative with plenty of crunch.
Herb Swap: If sage isn’t your favorite, try rosemary or thyme — they also pair wonderfully with squash.

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

Step 1: Roast the Squash

Start by preheating your oven to 425ºF. Slice the squash in half lengthwise and scoop out the seeds. I like to drizzle the cut sides with olive oil, then season generously with salt and pepper. Flip them cut-side down on your baking sheet so the skin gets nicely roasted. Roast for 20 to 25 minutes until you can easily pierce it with a fork—check at 20 minutes as squash sizes vary. This step is crucial for getting a tender base that holds its shape when filled.

Step 2: Caramelize the Shallots

While the squash roasts, melt butter in a skillet over medium heat. Add shallots and cook slowly, stirring often, until they turn golden and sweet — this usually takes 6 to 7 minutes. I turn the heat down to medium-low after the first few minutes to avoid burning — patience here really pays off. Stir in minced garlic and sage leaves and cook for 1-2 more minutes until fragrant. Don’t forget to season lightly with salt before removing from heat.

Step 3: Prepare the Filling

Once the squash halves are cool enough to handle, scoop out the flesh, keeping about a quarter-inch of the edge to hold its shape. Pop the scooped squash into a food processor along with the crème fraîche, maple syrup, and half the Parmesan cheese. Blend until silky smooth. Then fold in the caramelized shallot mixture — you want your filling to be creamy, aromatic, and just a bit sweet.

Step 4: Fill & Top

Spoon the filling evenly back into the squash shells — I like mine about two-thirds full so there’s space for the topping. For the pecan topping, mix chopped pecans, Panko breadcrumbs, the remaining Parmesan, olive oil, and a pinch of salt. Scatter this crunchy mixture generously over your filled squash. If you want to elevate things further, brush fresh sage leaves with oil and place them on top — a little crisp herbiness that really wows.

Step 5: Bake to Finish

Return the squash to the oven for another 15 minutes. You’re looking for a warm, bubbly filling and a golden, crisp topping. The aroma at this point is downright irresistible. Serve hot and enjoy every savory-sweet bite!

Top Tip

From my experience making this Twice-Baked Honeynut Squash with Pecan Topping Recipe, a few small adjustments make a world of difference. These tips saved me from common pitfalls and helped me perfect the balance of flavors.

Don’t rush the shallots: Slow caramelization is key — turning down the heat prevents bitterness and brings out natural sweetness.
Leave a border when scooping: Leaving that quarter-inch edge helps the squash boats hold their shape and avoids a messy bake.
Panko over regular breadcrumbs: It gives you that extra crisp topping that’s light and airy instead of dense.
Use fresh sage: Adding crispy fresh sage leaves on top just before baking really brightens the dish and makes it feel extra special.

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

Garnishes

I love adding a small sprinkling of extra chopped pecans and a few fresh sage leaves right after baking — it adds visual appeal and an extra hit of crunch and earthiness. A light drizzle of maple syrup over the top can be a nice touch if you’re feeling adventurous.

Side Dishes

This Twice-Baked Honeynut Squash makes a fabulous side for roast chicken or turkey, but I’ve also served it alongside quinoa salad or sautéed greens for a cozy vegetarian meal. It plays well with earthy root vegetables and even adds a lovely contrast to a tangy cranberry chutney.

Creative Ways to Present

I once served these squash boats in a shallow wooden box lined with fresh herbs at a dinner party — it created a rustic, inviting look. You can also scoop the filling into small ramekins or muffin tins for bite-sized appetizers. Either way, presentation is simple but feels special.

Make Ahead and Storage

Storing Leftovers

Leftover squash keeps beautifully in an airtight container in the fridge for up to 3 days. I recommend separating the topping from the squash if you expect the topping to get soggy — you can always re-toast it before serving again.

Freezing

This recipe freezes well if you want to prep ahead. I freeze the filled squash (without topping) wrapped tightly in foil or plastic wrap. To serve, thaw overnight in the fridge, add the topping fresh, and bake until warm and crispy.

Reheating

Reheat leftovers in the oven at 350ºF to preserve the texture, about 15 minutes. If you separated the topping, sprinkle it on for the last 5 minutes to keep it crisp. Avoid microwaving if you want to keep that crunchy topping intact.

Frequently Asked Questions:

Can I use butternut squash instead of honeynut?

Absolutely! While honeynut squash has a sweeter, more concentrated flavor, butternut squash works perfectly well and will yield similar creamy results.

How do I make this recipe dairy-free?

You can substitute the crème fraîche with coconut cream or a dairy-free cream cheese alternative, and use vegan butter for the shallot caramelization to make this recipe dairy-free without sacrificing flavor.

Can the pecan topping be made ahead?

Yes, you can prepare the pecan-Panko topping a day ahead and store it in an airtight container at room temperature. Add it right before baking for the best crunch.

What’s the best way to serve leftover twice-baked squash?

Leftovers reheat beautifully in the oven to refresh the crisp topping. They also make great additions to salads or can be gently mashed and served as a creamy side dish.

Final Thoughts

This Twice-Baked Honeynut Squash with Pecan Topping Recipe isn’t just a side dish, it’s a comforting celebration of fall’s best flavors that I’ve come to treasure for cozy family dinners and holiday feasts. I promise once you try it, you’ll find yourself making it again and again — it’s just that wholesome and satisfying. So go ahead, get cozy in your kitchen and give this recipe a whirl. I can’t wait to hear how you make it your own!