Spaghetti Squash Au Gratin Recipe

Sharing one of my all-time favorite comforting dishes with you today: Spaghetti Squash Au Gratin. This recipe brings together tender strands of roasted spaghetti squash in a rich, creamy cheese sauce, with a beautifully golden, crispy topping. Perfectly balanced, it’s a delightful way to enjoy vegetables with all the indulgence of a classic gratin. The trickiest part — and you’ll hear me say this a few times — is to pour the spaghetti squash mixture into a greased 9×13 inch baking dish just right so everything bakes evenly into cheesy perfection.

Ingredients You’ll Need

Don’t let the list intimidate you—these ingredients are simple, honest, and each plays an important role in making this dish sing with flavor and texture. From the buttery richness to the sharpness of the cheeses, every element shines.

• 1 large spaghetti squash (about 3-4 pounds): The star of the show, roasted until tender and shredded into spaghetti-like strands.
• 4 tablespoons unsalted butter, divided: Adds that luscious, creamy depth and helps build the sauce.
• 1 medium yellow onion, finely chopped: Provides subtle sweetness and complexity when sautéed.
• 2 cloves garlic, minced: A small amount packs an aromatic punch that warms up the entire dish.
• 4 tablespoons all-purpose flour: Essential for creating a smooth, thick roux to hold the sauce together.
• 3 cups whole milk: The creamy base that softens the cheeses and balances richness.
• 1/2 teaspoon salt, plus more to taste: Enhances all the natural flavors.
• 1/4 teaspoon black pepper, plus more to taste: For just the right touch of spice.
• 1/4 teaspoon nutmeg: A hint of warm spice that beautifully complements the creamy cheese sauce.
• 1 cup grated Gruyere cheese, divided: Adds a nutty, slightly sweet flavor that melts like a dream.
• 1 cup grated sharp cheddar cheese, divided: Brings a sharp, tangy contrast to the creamy sauce.
• 1/2 cup grated Parmesan cheese, divided: For that salty, umami kick both inside and on top.
• 1/4 cup panko breadcrumbs: Gives a delightful crunch to the gratin’s golden topping.
• 2 tablespoons chopped fresh parsley (optional): A fresh garnish that adds color and brightness when serving.

How to Make Pour the spaghetti squash mixture into a greased 9×13 inch baking dish

Step 1: Roast the Spaghetti Squash

Start by cutting your large spaghetti squash in half lengthwise and scooping out the seeds and stringy bits. Drizzle the cut sides with 2 tablespoons of melted butter, then season generously with salt and pepper. Placing the squash cut-side down on a lined baking sheet, roast it in a 400°F oven for 45 to 60 minutes. You’ll know it’s done when the flesh is tender and easily pierced with a fork. This step is key for soft, stringy strands that soak up the creamy sauce perfectly.

Step 2: Make the Creamy Cheese Sauce

While the squash cools enough to handle, melt the remaining 2 tablespoons of butter in a large saucepan. Sauté the finely chopped onion until translucent and soft, then add the minced garlic for just a minute until fragrant. Sprinkle in the flour, stirring constantly to build a roux—this thickens the sauce beautifully without lumps. Slowly whisk in the milk, keeping it smooth and creamy as it comes to a gentle simmer. Season with salt, black pepper, and a touch of nutmeg.

Step 3: Combine Cheese and Squash

Off the heat, stir in 3/4 cup each of Gruyere and cheddar and 1/4 cup Parmesan cheese until melted and silky. Then add the shredded spaghetti squash and gently fold everything together into a luscious, cheesy blend. Now for the important part—you want to pour the spaghetti squash mixture into a greased 9×13 inch baking dish carefully so the sauce and squash are evenly spread. This ensures your gratin bakes up perfectly.

Step 4: Prepare the Topping and Bake

Mix the remaining cheeses and panko breadcrumbs and sprinkle that hearty topping evenly over your spaghetti squash mixture. Place the dish in the oven and bake for 20 to 25 minutes until the topping is golden, crispy, and bubbling with cheesy goodness. After pulling it from the oven, allow it to rest a little so flavors settle before serving. Again, don’t forget to pour the spaghetti squash mixture into a greased 9×13 inch baking dish evenly to get that ideal crust and gooey center.

How to Serve Pour the spaghetti squash mixture into a greased 9×13 inch baking dish

Garnishes

I love to sprinkle freshly chopped parsley over the top just before serving. It adds a bright pop of color and freshness that lifts the rich, creamy flavors. A light drizzle of high-quality olive oil or a pinch of cracked black pepper also complements the gratin brilliantly.

Side Dishes

This Spaghetti Squash Au Gratin works wonderfully as a main dish or alongside something light and crisp. A simple green salad with a tangy vinaigrette or roasted Brussels sprouts balances the richness perfectly. If you want to add protein, grilled chicken or baked fish are excellent companions.

Creative Ways to Present

For a fun twist, try serving individual portions in small ramekins instead of one large dish. This helps maintain that golden crust on top and makes for a stunning presentation at dinner parties. You can also layer sautéed mushrooms or caramelized onions inside the gratin for additional depth and layers of flavor.

Make Ahead and Storage

Storing Leftovers

Leftover Spaghetti Squash Au Gratin stores beautifully in an airtight container in the fridge for up to 4 days. To keep the topping crisp, you might want to cover the dish with foil or transfer leftovers to a flat container before refrigerating.

Freezing

You can freeze leftovers for up to 2 months. Just be sure to let the dish cool completely, then wrap tightly with plastic wrap and foil before popping it into the freezer. When ready to enjoy, thaw it overnight in the fridge for best results.

Reheating

Reheat in a 350°F oven covered with foil for about 20 minutes until warmed through. Removing the foil in the last 5 minutes will help restore some of that crispy topping you love. Avoid microwaving if possible, as the texture can become soggy.

FAQs

Can I use a different type of squash?

This recipe specifically shines with spaghetti squash because of its unique strand-like texture when cooked. Using other squash may result in a different texture and less of the signature “spaghetti” effect.

Do I need to peel the squash?

No peeling is necessary. After roasting and shredding the flesh with a fork, the strands separate easily and the skin is discarded. The skin acts as a natural container during roasting.

Can I make this dish dairy-free?

While dairy adds the creamy richness that defines this gratin, you can experiment with plant-based milks and cheese alternatives. Just keep in mind the sauce’s texture and melting properties will differ.

Is it possible to make this gluten-free?

Yes! Substitute the all-purpose flour with a gluten-free flour blend or use cornstarch to thicken the sauce. Also, choose gluten-free panko or omit breadcrumbs for the topping if needed.

Can I prepare the squash ahead of time?

Absolutely! Roast and shred the spaghetti squash earlier in the day or even the day before. Keep it refrigerated until you’re ready to make the sauce and assemble the gratin.

Final Thoughts

I can’t recommend this Spaghetti Squash Au Gratin enough for anyone craving hearty comfort food with a veggie twist. Remember, the magic really happens when you pour the spaghetti squash mixture into a greased 9×13 inch baking dish evenly and top it with that crisp, cheesy crust. Give it a try and watch it become a staple in your home just like it is in mine!

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