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Spaghetti Squash Au Gratin

A creamy, cheesy comfort food featuring tender spaghetti squash strands coated in rich Gruyere-cheddar sauce, topped with a golden breadcrumb crust. This healthy twist on classic au gratin delivers restaurant-quality flavor.
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 300 kcal

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
 

  • Preparing the Spaghetti Squash:
  • Preheat oven to 400°F (200°C).
  • Cut spaghetti squash in half lengthwise and scoop out seeds. (Tip: Microwave whole squash for 2-3 minutes if too hard to cut.)
  • Drizzle cut sides with 2 tablespoons melted butter, season with salt and pepper.
  • Place halves cut-side down on parchment-lined baking sheet.
  • Roast for 45-60 minutes until fork-tender.
  • Let cool, then scrape flesh into spaghetti-like strands with a fork. Set aside.
  • Making the Cheese Sauce:
  • In large saucepan over medium heat, melt remaining 2 tablespoons butter.
  • Add chopped onion and cook 5-7 minutes until soft and translucent.
  • Add minced garlic and cook 1 minute until fragrant.
  • Sprinkle flour over mixture, stirring constantly for 1-2 minutes to create a roux.
  • Gradually whisk in milk, starting with small amounts to prevent lumps.
  • Bring to simmer over medium heat, stirring constantly.
  • Reduce heat to low and simmer 5-7 minutes until sauce thickens.
  • Remove from heat and season with salt, pepper, and nutmeg.
  • 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 cheese sauce, folding gently to combine.
  • Pour mixture into greased 9x13 inch baking dish.
  • In small bowl, combine remaining cheeses with panko breadcrumbs.
  • Sprinkle topping evenly over squash mixture.
  • Bake at 400°F for 20-25 minutes until golden brown and bubbly.
  • Let rest 5-10 minutes before serving.
  • Garnish with fresh parsley if desired.

Notes

Storage: Store leftovers in airtight container in refrigerator for 3-4 days. Reheat in oven at 350°F for 15-20 minutes or microwave for 2-3 minutes.
Freezing: Freeze assembled au gratin (without breadcrumb topping) for up to 2 months. Thaw overnight, add fresh topping, and bake as directed.
Make-Ahead: Assemble completely, cover with foil, and refrigerate up to 24 hours. Add 5-10 minutes to baking time.
Cheese Tips: Use block cheese and grate yourself for best melting. Pre-shredded cheese contains anti-caking agents that create grainy texture.
Variations:
Add cooked bacon, ham, or sausage for protein
Mix in sautéed mushrooms or wilted spinach
Substitute pepper jack for spicy version
Use gluten-free flour and breadcrumbs for gluten-free option
Vegetarian Note: Check that Parmesan doesn't contain animal rennet if making vegetarian.
Keyword baked spaghetti squash, spaghetti squash au gratin