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 magical about the season when you get to savor dishes like my Twice-Baked Honeynut Squash with Pecan Topping Recipe. It’s that perfect blend of creamy squash, rich sage, and a crunchy pecan topping that just makes your kitchen smell like home.

Five halves of roasted butternut squash are placed on a white plate with blue floral patterns, arranged to fill the plate. Each squash half shows bright orange flesh with a slightly caramelized surface, topped with a crumbly mixture of chopped nuts and breadcrumbs that add a crunchy texture. Green sage leaves are scattered on top of the crumb mixture, creating a contrast with the orange squash. The plate rests on a white marbled surface, and there are fresh sage leaves placed next to the squash on the plate. A woman’s hand is visible holding a piece of the plate, and a glass with a light brown drink is at the edge of the frame. 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 a few falls ago, and it quickly became my go-to for festive dinners. The combination of soft, buttery squash and that toasty pecan crunch is just addictive. Plus, it’s deceptively simple to make but sure to impress anyone at your table.

Balanced Texture: Creamy squash filling paired with a crispy pecan and panko topping adds delightful contrast.
Fresh Flavors: Aromatic sage and caramelized shallots elevate the depth of this dish beyond typical squash recipes.
Make-Ahead Friendly: You can prepare it in advance and simply reheat without losing its charm.
Versatile Side Dish: Perfect for holidays or cozy weeknight dinners, and pairs well with many mains.

Ingredients & Why They Work

Each ingredient in the Twice-Baked Honeynut Squash with Pecan Topping Recipe was thoughtfully chosen. The sweet, nutty squash meets savory and slightly sweet elements like shallots with maple syrup — it’s a harmony you don’t want to miss. When shopping, look for firm squash with vibrant orange skin and fresh sage leaves for the best results.

Flat lay of fresh whole honeynut squashes with smooth orange skin and green stems, a small white ceramic bowl of extra-virgin olive oil, a few whole uncracked brown eggs with clean shells, a small white ceramic bowl of kosher salt, a small white ceramic bowl of freshly ground black pepper, a small white ceramic bowl holding golden butter cubes, a small white ceramic bowl filled with thinly sliced pale pink shallots, a single garlic clove with its papery skin intact, fresh green sage leaves scattered neatly, 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 heaped with finely grated pale yellow Parmesan cheese, a small white ceramic bowl of chopped light brown pecans, a small white ceramic bowl of golden panko breadcrumbs 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, it roasts beautifully and has a creamy texture.
Extra-virgin olive oil: Adds fruitiness and richness, perfect for roasting and crisping the topping.
Kosher salt and black pepper: Essential for seasoning and balancing flavors throughout the dish.
Butter: Helps caramelize the shallots and brings a silky mouthfeel.
Shallots: Their mild onion flavor caramelizes into sweet, savory goodness.
Garlic: Adds depth and aroma without overpowering.
Fresh sage leaves: Robust and earthy, they brighten the filling and crisp up beautifully.
Crème fraîche (or cream cheese): Brings creaminess and slight tang to the squash filling.
Maple syrup: A drizzle adds natural sweetness that complements the squash.
Parmesan cheese: Provides a salty, nutty note and helps bind the filling and topping.
Pecans: Offer crunch and a buttery flavor that pairs perfectly with squash.
Panko breadcrumbs: Light and crispy, helping create that golden topping.

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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

One of the reasons I treasure this Twice-Baked Honeynut Squash with Pecan Topping Recipe is how easy it is to tweak. Whether you want a bit more spice or a dairy-free version, this recipe lets you play around and still come out with something delicious.

Variation: I’ve tried swapping the sage for fresh thyme and honestly loved the subtle difference it adds—great if you want a milder herbal note.
Dairy-Free Option: Use a vegan cream cheese substitute and skip the Parmesan or try a vegan cheese alternative to keep it creamy.
Extra Crunch: Toss some toasted pumpkin seeds with the pecan topping for a different texture.
Spicier Kick: Add a pinch of chili flakes or smoked paprika to the topping mix if you want to jazz it up.

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

Step 1: Roast the Honeynut Squash to Perfection

Start by preheating your oven to 425ºF. Slice your honeynut squashes lengthwise and scoop out the seeds—don’t toss them; they’re fun to roast later! Arrange the squash halves cut side down on a baking sheet, drizzle with half of your olive oil, and season with salt and pepper. Roasting them cut side down helps caramelize the skin just enough, while the flesh gets tender in about 20-25 minutes. Keep an eye on them and check at 20 minutes—you want them fork-tender but still holding their shape for scooping later.

Step 2: Caramelize Shallots with Sage and Garlic

While the squash is roasting, melt butter in a skillet over medium heat. Toss in the thinly sliced shallots and cook, stirring often. After a few minutes, lower the heat to medium-low—this keeps them from burning and lets their natural sugars caramelize beautifully over 6-7 minutes. Then add minced garlic and chopped sage leaves, cooking for another 1-2 minutes until fragrant. Don’t forget a pinch of salt to bring out all those layered flavors.

Step 3: Scoop and Blend Your Filling

When the squash has cooled just enough to handle, carefully scoop out most of the flesh, leaving a quarter-inch border so the skin acts as a little “bowl.” Pop the squash flesh into a food processor along with crème fraîche, maple syrup, and half of the Parmesan cheese. Blend it until smooth, then fold in the caramelized shallot mixture by pulsing a few times. This filling should be rich, creamy, and a little sweet with that hint of sage.

Step 4: Topping Time!

Combine chopped pecans, panko breadcrumbs, remaining Parmesan, and the other half of your olive oil in a small bowl, seasoning with a pinch of salt. This mixture becomes the crunch crown atop the squash. If you have extra sage leaves, toss them with olive oil and scatter them over the topping—they crisp up in the oven and add an irresistible aroma and bite.

Step 5: Bake Again to Finish

Fill each squash half evenly with your silky squash filling, sprinkle the pecan topping, and place back in the oven for about 15 minutes. You want the filling warmed through and that topping nice and golden. Keep an eye to avoid burning—once the topping crisps up, you’re good to go!

Top Tip

Over the years, I learned these little tricks to make the Twice-Baked Honeynut Squash with Pecan Topping Recipe truly shine. Trust me, these can save you time and frustration in the kitchen!

Roast Cut Side Down: Helps caramelize the skin and keeps moisture in the flesh for a tender scoop.
Lower Heat for Shallots: Reduces the risk of burning and develops a deeper, sweeter flavor.
Don’t Overfill: Leave a bit of room in the squash halves so the filling doesn’t spill over during the second bake.
Sage Leaves on Top: Adds crispy, herby garnish that tastes even better than it smells!

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

The image shows a white plate with blue floral patterns holding two halves of roasted squash. Each half has a bright orange, mashed filling with a creamy texture. On top, there is a crumbly, light golden brown topping mixed with small pieces of toasted nuts and a few whole dried leaves for garnish. A gold spoon is scooping some filling from one squash half, revealing its smooth, thick inside. The plate is on a white marbled surface. photo taken with an iphone --ar 2:3 --v 7

Garnishes

I love adding a few crispy sage leaves right on top as a garnish — it’s elegant and invites people to dive right in. A light drizzle of good-quality maple syrup or a sprinkle of flaky sea salt just before serving takes it up another notch. Sometimes, I toss on some fresh sage for color, too.

Side Dishes

This squash pairs beautifully with roasted chicken or turkey. It also complements a hearty grain salad or a fresh, crunchy green salad. For holiday dinners, I often serve it alongside mashed potatoes and green beans almondine—it balances the plate perfectly.

Creative Ways to Present

For special occasions, I arrange the filled squash halves on a large platter garnished with sage sprigs, fresh cranberries, and sometimes a swirl of cranberry sauce on the side. It makes for a beautiful, festive centerpiece everyone can admire before digging in.

Make Ahead and Storage

Storing Leftovers

Leftover twice-baked honeynut squash keeps well in an airtight container in the fridge for up to 3 days. I found that covering it tightly prevents the topping from getting soggy, so you can enjoy that crunch even on day two.

Freezing

While I personally prefer it fresh, this recipe freezes nicely. Wrap each squash half tightly in foil or plastic wrap, then place in a freezer-safe container. When ready to eat, thaw overnight and reheat in the oven to bring back the crisp topping.

Reheating

For best results, reheat in a preheated 375ºF oven for about 15-20 minutes. This revives the crispy pecan topping and warms the creamy filling evenly without making it soggy like a microwave would.

Frequently Asked Questions:

Can I use a different type of squash for this recipe?

Absolutely! Butternut squash is a great substitute if you can’t find honeynut squash. Just keep in mind that cooking times might be slightly longer because butternuts are bigger and denser. Adjust roasting time until the flesh is fork-tender before scooping out.

How do I make this recipe dairy-free?

You can swap out the crème fraîche for a plant-based cream cheese and use vegan butter instead of regular butter. For the Parmesan, try nutritional yeast or a dairy-free parmesan substitute. The pecan topping will still provide amazing crunch and flavor.

What’s the best way to store leftovers?

Store leftovers in an airtight container in the fridge. To keep the topping from getting soggy, I recommend placing a piece of parchment paper between the squash halves if stacking. Reheat in the oven to restore crispiness.

Can I prepare this recipe ahead of time?

Yes! You can roast the squash and prepare the filling a day ahead. Assemble the squash boats with filling and topping, cover them, and refrigerate. When ready to serve, bake until warm and the topping is golden. This makes entertaining a breeze.

Final Thoughts

Honestly, this Twice-Baked Honeynut Squash with Pecan Topping Recipe feels like a warm hug from the inside out. Whether you bring it to a fall gathering or treat yourself on a quiet evening, its cozy flavors never disappoint. I hope you enjoy making and sharing it as much as I do—it’s a little bit of autumn magic in every bite.