Three-Cheese Spaghetti Squash Gratin

Roasted spaghetti squash tossed with a creamy three-cheese sauce made from Monterey Jack, Gruyere, and Parmesan, combined with crispy bacon and baked until bubbly and golden. A satisfying vegetable-forward gratin with rich, savory depth from the béchamel base and nutmeg seasoning.
Ingredients
- 1 large spaghetti squash, about 3 lbs
- 6 slices bacon, Monterey Jack or Hickory Smoked
- ½ cup Monterey Jack cheese, shredded
- ½ cup Gruyere cheese, shredded
- ¼ cup Parmesan cheese, grated
- 2 Tbsp unsalted butter
- 3 Tbsp all-purpose flourcornstarch1:1 by weightthickenergluten-free
gluten-free alternative
- 2 cups milk
- 1 tsp kosher salt
- ½ tsp black pepper, freshly ground
- ¼ tsp nutmeg, freshly grated
Instructions
- 1
Preheat oven to 350 F.
- 2
Cut squash in half lengthwise and remove seeds and fiber with a spoon.
- 3
Place squash cut-side down on a lightly greased baking sheet and bake until tender when pierced with a fork, about 40 minutes.
- 4
Cook bacon in the oven alongside the squash until done, then crumble.
- 5
Cool squash until handleable, then scrape strands from shell into a large bowl.
- 6
Mix cheeses together and grease a 2-quart baking dish.
- 7
Melt butter in a medium saucepan over medium-high heat.
- 8
Whisk in flour, salt, pepper, and nutmeg, cooking while whisking until the flour smells cooked, about 3 minutes.
- 9
Slowly pour in milk while whisking continuously.
- 10
Reduce heat to medium and continue whisking until mixture thickens slightly, about 3 minutes.
- 11
Remove from heat and stir in half the cheese mixture until melted.
- 12
Pour cheese sauce over squash and stir to combine.
- 13
Transfer mixture to prepared baking dish.
- 14
Sprinkle remaining cheese mixture and bacon on top.
- 15
Bake until bubbling and brown on top, about 30 minutes.
Tips
Squash and bacon can bake simultaneously to save time.
Cook the flour roux until fragrant to eliminate raw flour taste in the sauce.
Whisk milk in slowly to prevent lumps in the béchamel.
Reserve half the cheese for topping to ensure a golden, crispy surface.
Good to Know
Cover and refrigerate up to 3 days. Reheat covered at 350 F until warmed through.
Assemble gratin through topping step, cover, and refrigerate up to 1 day before baking.
Serve directly from baking dish while hot and bubbling.
Common Mistakes
Do not skip cooling the squash to prevent breaking strands during scraping.
Do not add milk too quickly to the roux to avoid lumpy sauce.
Do not skip cooking the roux until fragrant to eliminate raw flour taste.