Spaghetti Squash Au Gratin Recipe
Introduction
Spaghetti Squash Au Gratin is a comforting and healthy twist on the classic cheesy casserole. This dish pairs tender roasted spaghetti squash with a creamy cheese sauce and a crisp golden topping. Perfect as a satisfying side or a light main course.

Ingredients
- 1 large spaghetti squash (about 3-4 pounds)
- 4 tablespoons unsalted butter, divided
- 1 medium yellow onion, finely chopped
- 2 cloves garlic, minced
- 4 tablespoons all-purpose flour
- 3 cups whole milk
- 1/2 teaspoon salt, plus more to taste
- 1/4 teaspoon black pepper, plus more to taste
- 1/4 teaspoon nutmeg
- 1 cup grated Gruyere cheese, divided
- 1 cup grated sharp cheddar cheese, divided
- 1/2 cup grated Parmesan cheese, divided
- 1/4 cup panko breadcrumbs
- 2 tablespoons chopped fresh parsley, for garnish (optional)
Instructions
- Step 1: Preheat the oven to 400°F (200°C).
- Step 2: Cut the spaghetti squash in half lengthwise and scoop out the seeds and stringy bits.
- Step 3: Drizzle the cut sides of the squash with 2 tablespoons of melted butter and sprinkle generously with salt and pepper.
- Step 4: Place the squash halves cut-side down on a parchment-lined baking sheet and roast for 45-60 minutes until tender and easily pierced with a fork.
- Step 5: Let the squash cool slightly, then use a fork to shred the flesh into spaghetti-like strands. Set aside.
- Step 6: In a large saucepan over medium heat, melt the remaining 2 tablespoons of butter.
- Step 7: Add the chopped onion and cook until softened and translucent, about 5-7 minutes. Stir in the garlic and cook for another minute until fragrant.
- Step 8: Sprinkle the flour over the onion and garlic, stirring constantly for 1-2 minutes to make a roux.
- Step 9: Gradually whisk in the milk, ensuring the sauce stays smooth and lump-free.
- Step 10: Bring the sauce to a simmer over medium heat, then reduce to low and cook for 5-7 minutes until slightly thickened.
- Step 11: Stir in salt, pepper, and nutmeg. Taste and adjust seasoning as needed.
- Step 12: Remove from heat and stir in 3/4 cup Gruyere, 3/4 cup cheddar, and 1/4 cup Parmesan until melted and creamy. Reserve the remaining cheese for topping.
- Step 13: Gently fold the shredded spaghetti squash into the cheese sauce.
- Step 14: Transfer the mixture to a greased 9×13 inch baking dish.
- Step 15: In a small bowl, combine the remaining 1/4 cup Gruyere, 1/4 cup cheddar, 1/4 cup Parmesan, and panko breadcrumbs.
- Step 16: Evenly sprinkle the cheese and breadcrumb mixture over the squash.
- Step 17: Bake for 20-25 minutes until the topping is golden brown and bubbly.
- Step 18: Remove from oven and let rest for 5-10 minutes before serving.
- Step 19: Garnish with chopped fresh parsley if desired. Serve hot and enjoy!
Tips & Variations
- For a richer sauce, substitute half the milk with heavy cream.
- Try adding cooked bacon or sautéed mushrooms for extra flavor.
- Use gluten-free flour and breadcrumbs to make this dish gluten-free.
- Fresh thyme or rosemary can be added to the sauce for a herbal note.
- Ensure the spaghetti squash is roasted until very tender for the best texture.
Storage
Store leftovers in an airtight container in the refrigerator for up to 3 days. Reheat gently in the oven or microwave until warmed through. To maintain a crispy topping, reheating in the oven is recommended.
How to Serve

Serve this delicious recipe with your favorite sides.
FAQs
Can I use a different type of cheese?
Yes, you can substitute Gruyere and cheddar with other melting cheeses like mozzarella or fontina, but the flavor will vary slightly.
How do I know when the spaghetti squash is done roasting?
The squash is ready when it is easily pierced with a fork and the flesh feels tender. It should pull apart easily into strands.
PrintSpaghetti Squash Au Gratin Recipe
This Spaghetti Squash Au Gratin offers a deliciously creamy and cheesy twist on a healthy vegetable base. Roasted spaghetti squash strands are enveloped in a rich Gruyere, cheddar, and Parmesan cheese sauce, then baked with a crunchy panko breadcrumb topping. It’s a comforting, low-carb alternative to traditional au gratin dishes, perfect as a side or a main for those seeking a nutritious yet indulgent meal.
- Prep Time: 15 minutes
- Cook Time: 1 hour 10 minutes
- Total Time: 1 hour 25 minutes
- Yield: 6 servings 1x
- Category: Side Dish
- Method: Baking
- Cuisine: American
- Diet: Vegetarian
Ingredients
Spaghetti Squash
- 1 large spaghetti squash (about 3–4 pounds)
- 2 tablespoons unsalted butter, melted (for squash)
- Salt and freshly ground black pepper, to taste
Cheese Sauce
- 2 tablespoons unsalted butter
- 1 medium yellow onion, finely chopped
- 2 cloves garlic, minced
- 4 tablespoons all-purpose flour
- 3 cups whole milk
- 1/2 teaspoon salt
- 1/4 teaspoon black pepper
- 1/4 teaspoon ground nutmeg
- 3/4 cup grated Gruyere cheese
- 3/4 cup grated sharp cheddar cheese
- 1/4 cup grated Parmesan cheese
Topping
- 1/4 cup grated Gruyere cheese
- 1/4 cup grated sharp cheddar cheese
- 1/4 cup grated Parmesan cheese
- 1/4 cup panko breadcrumbs
Garnish
- 2 tablespoons chopped fresh parsley (optional)
Instructions
- Preheat the oven: Set the oven to 400°F (200°C) to ensure it reaches the perfect temperature for roasting the squash and baking the au gratin.
- Prepare the squash: Cut the spaghetti squash in half lengthwise and scoop out the seeds and fibrous strands from the center to create clean halves ready for roasting.
- Season the squash: Drizzle the cut sides of the squash with 2 tablespoons of melted butter, and generously season with salt and pepper to enhance flavor during roasting.
- Roast the squash: Place the squash halves cut-side down on a parchment-lined baking sheet and roast for 45-60 minutes until the flesh is tender and easily pierced with a fork.
- Shred the squash: Once the squash is cool enough to handle, use a fork to scrape out the flesh into spaghetti-like strands and set aside.
- Melt butter for sauce: In a large saucepan over medium heat, melt the remaining 2 tablespoons of butter to start the cheese sauce base.
- Sauté onion and garlic: Add the finely chopped onion to the melted butter and cook for 5-7 minutes until softened and translucent. Stir in minced garlic and cook for another minute until fragrant.
- Make the roux: Sprinkle the flour over the onion and garlic mixture and cook while stirring constantly for 1-2 minutes, which helps thicken the sauce later.
- Whisk in milk: Gradually pour in the milk, whisking continuously to avoid lumps and achieve a smooth sauce consistency.
- Simmer the sauce: Bring the sauce to a gentle simmer, stirring constantly, then reduce heat to low and cook for 5-7 minutes until it thickens slightly.
- Season the sauce: Stir in salt, black pepper, and nutmeg. Taste and adjust seasoning if necessary to balance the flavors.
- Add cheeses: Remove the saucepan from heat and fold in 3/4 cup Gruyere, 3/4 cup cheddar, and 1/4 cup Parmesan until the cheese melts into a smooth, creamy sauce.
- Combine squash with sauce: Gently stir the shredded spaghetti squash into the cheese sauce until well combined.
- Transfer to baking dish: Pour the mixture into a greased 9×13 inch baking dish, spreading it evenly.
- Prepare topping: In a small bowl, mix together the remaining 1/4 cup Gruyere, 1/4 cup cheddar, 1/4 cup Parmesan, and panko breadcrumbs for a flavorful crispy topping.
- Sprinkle topping: Evenly distribute the cheese and breadcrumb mixture over the surface of the squash casserole.
- Bake au gratin: Place the dish in the preheated oven and bake for 20-25 minutes until the topping is golden brown and bubbly.
- Rest before serving: Remove from the oven and let rest for 5-10 minutes to set the dish and enhance flavors.
- Garnish and serve: Optionally sprinkle with fresh chopped parsley, then serve hot and enjoy this creamy, cheesy, healthy casserole.
Notes
- To easily remove seeds from spaghetti squash, use a spoon and scrape gently.
- For a lighter version, substitute low-fat milk and reduce cheese quantities.
- Panko breadcrumbs add extra crunch—regular breadcrumbs can be used but with less crispiness.
- Allowing the au gratin to rest after baking helps it firm up, making serving easier.
- This dish can be prepared ahead up to the baking step and refrigerated, then baked before serving.
Keywords: spaghetti squash au gratin, cheesy spaghetti squash, healthy au gratin recipe, vegetarian casserole, low-carb comfort food

