Spaghetti Squash Au Gratin Recipe
Introduction
This Spaghetti Squash Au Gratin is a creamy, cheesy dish that offers a healthy twist on traditional au gratin recipes. It’s perfect for anyone looking to enjoy comfort food with fewer carbs and plenty of flavor.

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 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 with 2 tablespoons melted butter and sprinkle generously with salt and pepper.
- Step 4: Place 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: Once cool enough to handle, shred the squash flesh into spaghetti-like strands using a fork. Set aside.
- Step 6: In a large saucepan over medium heat, melt the remaining 2 tablespoons butter.
- Step 7: Add chopped onion and cook until softened and translucent, about 5-7 minutes. Add garlic and cook for an additional minute until fragrant.
- Step 8: Sprinkle flour over the onion and garlic mixture and cook, stirring constantly, for 1-2 minutes to form a roux.
- Step 9: Gradually whisk in the milk, ensuring no lumps form, until the sauce is smooth.
- Step 10: Bring the sauce to a simmer over medium heat, stirring constantly. Reduce heat to low and simmer for 5-7 minutes until slightly thickened.
- Step 11: Stir in salt, pepper, and nutmeg. Adjust seasonings to taste.
- 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 remaining cheese for topping.
- Step 13: Gently fold shredded spaghetti squash into the cheese sauce.
- Step 14: Pour the mixture into a greased 9×13 inch baking dish.
- Step 15: In a small bowl, combine remaining 1/4 cup Gruyere, 1/4 cup cheddar, 1/4 cup Parmesan, and panko breadcrumbs.
- Step 16: Sprinkle the cheese and breadcrumb mixture evenly over the squash.
- Step 17: Bake for 20-25 minutes until topping is golden brown and bubbly.
- Step 18: Remove from oven and let rest for 5-10 minutes.
- Step 19: Garnish with chopped fresh parsley if desired. Serve hot and enjoy!
Tips & Variations
- For a richer flavor, substitute half the milk with cream.
- Try adding cooked bacon or sautéed mushrooms to the cheese sauce for extra texture.
- Use gluten-free flour and breadcrumbs to make this dish gluten-free.
- Leftovers can be topped with extra cheese before reheating for a fresh, cheesy finish.
Storage
Store leftover au gratin in an airtight container in the refrigerator for up to 3 days. Reheat in the oven at 350°F (175°C) until warmed through to maintain the topping’s crispness. You can also reheat in the microwave, but the topping may soften.
How to Serve

Serve this delicious recipe with your favorite sides.
FAQs
Can I prepare this dish in advance?
Yes, you can assemble the dish up to the baking step, cover it, and refrigerate for up to 24 hours before baking.
What can I use if I don’t have Gruyere cheese?
Swiss cheese or mozzarella are good substitutes that melt well and offer a mild flavor similar to Gruyere.
PrintSpaghetti Squash Au Gratin Recipe
This Spaghetti Squash Au Gratin recipe offers a delightful and healthy twist on traditional au gratin dishes. Roasted spaghetti squash strands are combined with a creamy cheese sauce made from Gruyere, sharp cheddar, and Parmesan cheeses, then baked to golden perfection with a crispy breadcrumb topping. Ideal for a comforting yet nutritious meal, it’s rich in flavor while being lower in carbs than classic potato gratins.
- Prep Time: 15 minutes
- Cook Time: 80 minutes
- Total Time: 1 hour 35 minutes
- Yield: 6 servings 1x
- Category: Main Course
- Method: Baking
- Cuisine: American
Ingredients
Squash
- 1 large spaghetti squash (about 3–4 pounds)
- 2 tablespoons unsalted butter, melted
- Salt, to taste
- 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 (optional)
- 2 tablespoons chopped fresh parsley
Instructions
- Preheat Oven: Preheat your oven to 400°F (200°C) to get it ready for roasting the squash.
- Prepare the Squash: Cut the spaghetti squash in half lengthwise and scoop out the seeds and stringy bits from the center.
- Season the Squash: Drizzle 2 tablespoons of melted butter over the cut sides of the squash, then season generously with salt and black pepper.
- Roast the Squash: Place the squash halves cut-side down on a parchment-lined baking sheet. Roast for 45-60 minutes until the squash flesh is tender and easily pierced with a fork.
- Shred the Squash: Let the squash cool enough to handle, then use a fork to scrape out and shred the flesh into spaghetti-like strands. Set aside.
- Melt Butter: In a large saucepan over medium heat, melt the remaining 2 tablespoons of butter.
- Sauté Onion and Garlic: Add the finely chopped onion and cook for about 5-7 minutes until softened and translucent. Stir in the minced garlic and cook for an additional minute until fragrant.
- Make the Roux: Sprinkle the flour evenly over the onion and garlic mixture. Stir constantly and cook for 1-2 minutes to form a roux.
- Whisk in Milk: Gradually pour in the milk while whisking constantly to prevent lumps, creating a smooth sauce.
- Simmer the Sauce: Bring the sauce to a simmer over medium heat, stirring continuously. Then reduce the heat to low and simmer for 5-7 minutes until the sauce thickens slightly.
- Season the Sauce: Stir in 1/2 teaspoon salt, 1/4 teaspoon black pepper, and 1/4 teaspoon nutmeg. Taste and adjust the seasoning if necessary.
- Add Cheese: Remove the saucepan from heat and stir in 3/4 cup Gruyere, 3/4 cup sharp cheddar, and 1/4 cup Parmesan cheese until melted and the sauce is creamy.
- Combine Squash and Sauce: Gently fold the shredded spaghetti squash into the cheese sauce, mixing until fully combined.
- Transfer to Baking Dish: Pour the squash mixture into a greased 9×13 inch baking dish, spreading 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.
- Sprinkle Topping: Evenly distribute the cheese and breadcrumb mixture over the squash in the baking dish.
- Bake Au Gratin: Place the dish in the preheated oven and bake for 20-25 minutes until the topping is golden brown and bubbly.
- Let it Rest: Remove the dish from the oven and let it rest for 5-10 minutes to set.
- Garnish and Serve: Sprinkle with fresh chopped parsley if desired. Serve hot and enjoy your healthy, cheesy spaghetti squash au gratin!
Notes
- You can substitute whole milk with 2% milk for a lighter option.
- Ensure to roast the spaghetti squash cut-side down for moist, tender strands.
- For gluten-free, substitute the all-purpose flour with a gluten-free flour blend and use gluten-free breadcrumbs.
- The nutmeg adds warmth and depth to the cheese sauce but can be omitted if preferred.
- This dish reheats well and can be stored in the refrigerator for up to 3 days.
Keywords: spaghetti squash, au gratin, healthy cheesy casserole, low carb side dish, roasted squash recipe

