Name: Twice-Baked Honeynut Squash 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 (substitute 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 fall flavors in my Twice-Baked Honeynut Squash Recipe. Roasting the squash brings out its natural sweetness, and the creamy, cheesy filling with a crispy pecan topping is absolutely irresistible. Trust me, this one’s worth rolling up your sleeves for!

Five halves of roasted butternut squash are arranged on a white plate with blue floral patterns, placed on a white marbled surface. Each squash half has a bright orange, soft flesh base topped with a crunchy mixture of chopped nuts and golden brown breadcrumbs, creating a textured, slightly rough layer. Scattered on top are small green fresh sage leaves adding a touch of color contrast. The squash edges are slightly caramelized with a warm brown hue, giving depth to the dish. A few fresh sage sprigs lie on the plate around the squash halves, and a glass of amber liquid is visible beside the plate. 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 Recipe
Top Tip
How to Serve Twice-Baked Honeynut Squash Recipe
Make Ahead and Storage
Frequently Asked Questions:
Final Thoughts
Twice-Baked Honeynut Squash Recipe

Why You'll Love This Recipe

I’m all about side dishes that start conversations at the table, and this Twice-Baked Honeynut Squash Recipe does exactly that. It’s cozy, festive, and every bite feels like a little celebration of fall.

Deep, Sweet Flavor: Roasting the honeynut squash caramelizes its sugar, giving a natural sweetness that's way better than any canned alternative.
Perfect Balance of Creamy and Crunchy: The filling is silky smooth, thanks to crème fraîche and parmesan, but the pecan-panko topping adds a satisfying crisp.
Simple Ingredient List: You don’t need anything fancy — just a few fresh, quality ingredients you might already have on hand.
Looks Impressive, Feels Like a Treat: These twice-baked boats are not only tasty but also make a gorgeous centerpiece for any meal.

Ingredients & Why They Work

All the ingredients in this Twice-Baked Honeynut Squash Recipe pull double duty—each one adds flavor and texture that build on the squash’s natural goodness. Here’s a quick rundown of why these ingredients shine together, and some shopping tips to get the best results.

Flat lay of a trio of whole fresh honeynut squashes with deep orange skin, a small white ceramic bowl of golden extra-virgin olive oil, a whole uncracked brown egg, a small mound of smooth pale butter, a neat pile of thinly sliced shallots, a single peeled garlic clove, a small bunch of fresh green sage leaves, a small white ceramic bowl of creamy off-white crème fraîche, a small white ceramic bowl of rich amber maple syrup, a small white ceramic bowl of finely grated pale yellow Parmesan cheese, a small white ceramic bowl filled with chopped glossy pecans, a small white ceramic bowl containing light golden Panko breadcrumbs, and a small white ceramic bowl with coarse kosher salt and fresh cracked black peppercorns scattered nearby, 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 your typical butternut, it roasts faster and has a gorgeous, deep orange flesh that’s naturally creamy.
Extra-Virgin Olive Oil: Adds richness and a subtle fruitiness, helping those squash halves roast up golden and tender.
Kosher Salt and Black Pepper: Essential for seasoning layers, letting the natural flavors of the squash and shallots come through.
Butter: For caramelizing shallots, deepening their sweetness and adding a silky mouthfeel to the filling.
Shallots: Milder and sweeter than onions, they caramelize beautifully and add a delicate savory note.
Garlic: Just a touch, to make the aroma pop without overpowering the dish.
Fresh Sage: The herbal aroma is the perfect autumnal accent and pairs wonderfully with squash and cheese.
Crème Fraîche: Blends into the squash to create a smooth, tangy richness. Softened cream cheese works well as a handy alternative.
Maple Syrup: A little natural sweetness to balance the savory elements, enhancing that cozy fall vibe.
Parmesan Cheese: Adds sharp, salty depth and helps bind the filling, plus creates a lovely crust with the topping.
Pecans: Provide crunch and a buttery nuttiness that complements the squash’s sweetness.
Panko Breadcrumbs: Bring light, crispy texture to the topping without weighing it down.

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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 Recipe is wonderfully versatile. I’ve played around with tweaking the toppings and fillings in different seasons, and I encourage you to make it your own. A little creativity goes a long way here.

Variation: I once swapped out pecans for toasted walnuts and swapped the sage for rosemary — the herby twist was fantastic for a Christmas dinner!
Dairy-Free Option: Use coconut cream instead of crème fraîche and nutritional yeast in place of Parmesan. It’s surprisingly good.
Extra Protein: Stir in cooked quinoa or crumbled sausage into the filling for a heartier main dish version.
More Sweetness: Adding a dash more maple syrup or even a touch of cinnamon can give it a cozy dessert-like edge the kids love.

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

Step 1: Roast the Honeynut Squash to Perfection

First things first: preheat your oven to 425ºF. Slice the honeynut squash in half lengthwise—don’t forget to scoop out those seeds! Lay the halves cut side down on a rimmed baking sheet, drizzle with 2 tablespoons of olive oil and season with kosher salt and pepper. This cut-side-down roasting steams the insides to softness while caramelizing the skin edges. After 20 to 25 minutes, poke with a fork—when it’s fork-tender, you’re good to go. The size of your squashes might shift the time a bit, so keep an eye on them.

Step 2: Caramelize Shallots for Sweet Savory Flavor

While the squash roasts, melt butter in a skillet over medium heat and add your thinly sliced shallots. This is a key flavor bomb, so be patient! Stir often to gently caramelize them—about 6 to 7 minutes. I usually dial down the heat to medium-low after a couple minutes so they don’t brown too fast. When they are soft and golden, toss in the garlic and chopped sage, cooking for 1 to 2 more minutes until fragrant. Season lightly with salt, then remove from heat.

Step 3: Prepare the Creamy Filling

Take your roasted squash out of the oven and let it cool just enough to handle safely. Scoop most of the warm squash flesh into a food processor, leaving about a ¼ inch border so the shells keep their shape. Add crème fraîche, maple syrup, and half of the grated Parmesan cheese. Blend everything smooth, then mix in that luscious shallot mixture by pulsing a few times. The filling should be creamy, aromatic, and perfectly balanced. Spoon it evenly back into the squash halves — if you prefer them extra-filled, just fill five halves and save or discard the sixth.

Step 4: Add the Nutty Crispy Topping

Mix together your finely chopped pecans, panko, the rest of the Parmesan, olive oil, and a pinch of salt in a small bowl. This topping is what takes the dish from good to showstopper. If you love sage like I do, rub a few extra leaves with olive oil and add them on top for a crispy, aromatic garnish. Scatter this over each filled squash boat, then it’s ready for the final bake.

Step 5: Bake Until Golden and Bubbling

Slide your squash back into the oven for about 15 minutes at 425ºF. You want the filling warmed through and the topping nice and golden with some crunch. Keep an eye on it the last few minutes so the breadcrumbs don’t burn. Once done, these babies are ready to wow your guests or yourself!

Top Tip

After making this Twice-Baked Honeynut Squash Recipe many times, a few little tricks really helped me nail the balance of textures and flavors every time. These tips will save you from common pitfalls and help your dish shine.

Roasting Cut Side Down: This keeps the flesh moist and tender while giving just the right caramelization around the edges.
Caramelize Shallots Low and Slow: Starting at medium, then lowering the heat stops them from burning and brings out their natural sweetness.
Leave a Border When Scooping: Keeping some flesh around the edge ensures your squash halves don’t collapse when baking a second time.
Toast Pecans Before Chopping: If time allows, lightly toast your pecans for a deeper nutty flavor that elevates the topping.

How to Serve Twice-Baked Honeynut Squash Recipe

Garnishes

I usually top mine with a few crispy fried sage leaves—it’s such a simple touch but adds freshness and complexity. Sometimes I sprinkle a little extra parmesan over the top right after baking. A drizzle of good-quality maple syrup before serving can also heighten the cozy sweetness if you’re feeling indulgent.

Side Dishes

This twice-baked treat pairs beautifully with roasted turkey or ham, but I’ve also served it alongside warm grain salads or sautéed greens like kale or spinach to round out the plate. Its richness makes it a perfect balance to crisp, acidic sides—think a bright arugula salad with a lemon vinaigrette.

Creative Ways to Present

For holiday dinners, I like arranging each squash half on a rustic wooden board, garnished with extra sage sprigs and a dusting of fresh cracked black pepper. It looks so inviting and gives you that “rustic gourmet” vibe. For family meals, I sometimes scoop the filling into ramekins for a fun twist on serving.

Make Ahead and Storage

Storing Leftovers

Once your twice-baked honeynut squash cools completely, wrap tightly in plastic wrap or place in an airtight container. It keeps well in the fridge for up to 3 days. I recommend reheating gently in the oven to maintain that crispy topping.

Freezing

I’ve frozen leftovers in sealed containers with decent results. To freeze fresh batches, let them cool after the final bake, then wrap tightly in foil and freeze. Reheat directly from frozen in a 350ºF oven until warmed through, adding a few extra minutes if needed for crispness.

Reheating

Microwaving is tempting, but you’ll lose that crunchy top. I always reheat mine in a 350ºF oven for about 15 minutes, covered loosely with foil at first to keep moisture, then uncovered at the end to revive the golden topping.

Frequently Asked Questions:

Can I make this Twice-Baked Honeynut Squash Recipe vegan?

Absolutely! Swap out the butter for a plant-based alternative, use coconut cream or cashew cream instead of crème fraîche, and replace Parmesan with nutritional yeast or a vegan cheese. Toast the pecans well for extra flavor.

How do I know when the honeynut squash is done roasting?

You want the squash to be fork-tender but not mushy. Roast cut side down at 425ºF and test around the 20-minute mark by inserting a fork into the flesh. It should slide in easily without resistance.

Can I prepare this recipe ahead of time?

Yes! You can roast and scoop the squash a day ahead, prepare the filling and topping, then assemble and bake it just before serving. Alternatively, fully bake and then reheat gently as needed.

What can I substitute for crème fraîche?

If you don’t have crème fraîche, softened cream cheese works beautifully. You could also mix sour cream or Greek yogurt for a similar tang and creaminess, but crème fraîche has a unique richness that really elevates the dish.

Final Thoughts

This Twice-Baked Honeynut Squash Recipe holds a special place in my heart as my go-to autumn showstopper. Every time I make it, the cozy aroma fills the kitchen and the combination of textures delights everyone at the table. I hope you’ll enjoy making it just as much as I do—it’s one of those recipes that feels fancy but is really all about simple, fresh ingredients and a little love. Give it a try, and don’t be surprised if it becomes your favorite fall side dish as well!