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Spaghetti Squash Au Gratin

Creamy, cheesy spaghetti squash au gratin with Gruyere, cheddar, and Parmesan. A healthier take on classic comfort food with a golden breadcrumb topping.
Prep Time 15 minutes
Cook Time 1 hour 10 minutes
Total Time 1 hour 25 minutes
Course Main Course, Side Dish
Cuisine American, French
Servings 6
Calories 350 kcal

Ingredients
  

  • For the Spaghetti Squash:
  • 1 large spaghetti squash about 3-4 pounds
  • 2 tablespoons unsalted butter melted
  • Salt and black pepper to taste
  • For the 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 plus more to taste
  • 1/4 teaspoon black pepper plus more to taste
  • 1/4 teaspoon nutmeg
  • 3/4 cup grated Gruyere cheese
  • 3/4 cup grated sharp cheddar cheese
  • 1/4 cup grated Parmesan cheese
  • For the 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
  • For Garnish:
  • 2 tablespoons fresh parsley chopped, optional

Instructions
 

  • Preparing the Spaghetti Squash:
  • Preheat oven to 400°F (200°C).
  • Cut the spaghetti squash in half lengthwise. If too hard, microwave for 2-3 minutes to soften. Scoop out seeds and stringy bits.
  • Drizzle each half with 2 tablespoons melted butter. Season generously with salt and pepper.
  • Place squash halves cut-side down on a parchment-lined baking sheet. Roast for 45-60 minutes until tender and easily pierced with a fork.
  • Let cool for 10 minutes. Use a fork to scrape the flesh into spaghetti-like strands. Transfer to a large bowl and set aside.
  • Making the Cheese Sauce:
  • In a large saucepan over medium heat, melt the remaining 2 tablespoons butter.
  • Add chopped onion and cook for 5-7 minutes until softened and translucent.
  • Add minced garlic and cook for 1 minute, stirring constantly, until fragrant.
  • Sprinkle flour over the onion and garlic. Stir constantly for 1-2 minutes to create a roux.
  • Gradually whisk in milk, about 1/2 cup at a time, whisking vigorously after each addition to prevent lumps.
  • Bring sauce to a gentle simmer over medium heat, stirring constantly. Reduce heat to low and simmer for 5-7 minutes until thickened.
  • Season with salt, pepper, and nutmeg. Taste and adjust seasonings.
  • Remove from heat. Stir in 3/4 cup Gruyere, 3/4 cup cheddar, and 1/4 cup Parmesan until melted and smooth.
  • Assembling and Baking:
  • Add shredded spaghetti squash to the cheese sauce. Fold gently to coat every strand evenly.
  • Pour mixture into a greased 9x13 inch baking dish. Spread evenly with a spatula.
  • In a small bowl, combine remaining cheeses and panko breadcrumbs. Sprinkle evenly over the squash mixture.
  • Bake at 400°F for 20-25 minutes until topping is golden brown and sauce is bubbling around the edges.
  • Remove from oven and let rest for 5-10 minutes. Garnish with chopped fresh parsley if desired. Serve hot.

Notes

Make-Ahead Instructions: Assemble the dish completely up to 24 hours in advance. Cover tightly with plastic wrap and refrigerate. Add 5-10 minutes to baking time when cooking from cold.
Storage: Store leftovers in an airtight container in the refrigerator for 3-4 days. Reheat in the oven at 350°F for 15-20 minutes (covered with foil) or microwave individual portions for 1-2 minutes.
Cheese Substitutions: Swiss cheese can replace Gruyere. Fontina or smoked gouda also work well. For a budget-friendly option, use all cheddar.
Gluten-Free Option: Use a 1:1 gluten-free flour blend in place of all-purpose flour for the roux.
Protein Additions: Stir in cooked bacon bits, diced ham, or shredded rotisserie chicken to make it a complete main course.
Don't Overcook the Squash: Check for doneness at 45 minutes. Overcooked squash becomes mushy and watery.
Use Freshly Grated Cheese: Pre-shredded cheese contains anti-caking agents that prevent smooth melting. Grate your own for best results.
Prevent Grainy Sauce: Always remove the pan from heat before adding cheese to prevent it from becoming grainy or separating.
Freezing: Can be frozen for up to 2 months in an airtight container. Thaw overnight in refrigerator before reheating.
Keyword healthy comfort food, spaghetti squash au gratin