Spaghetti Squash Mac Cheese (Printable)

Roasted spaghetti squash in a creamy two-cheese sauce creates a lighter, gluten-free take on the beloved classic.

# What You Need:

→ Vegetables

01 - 1 medium spaghetti squash (about 2.5 lbs)

→ Cheese Sauce

02 - 2 tablespoons unsalted butter
03 - 2 tablespoons gluten-free all-purpose flour (or regular all-purpose flour if not gluten-free)
04 - 1½ cups whole milk
05 - 1 teaspoon Dijon mustard
06 - ½ teaspoon garlic powder
07 - ½ teaspoon onion powder
08 - ½ teaspoon kosher salt
09 - ¼ teaspoon ground black pepper
10 - 1½ cups sharp cheddar cheese, shredded
11 - ½ cup Gruyère cheese, shredded (optional, for extra depth of flavor)

→ Topping

12 - 2 tablespoons grated Parmesan cheese
13 - ¼ cup gluten-free breadcrumbs (or regular breadcrumbs if not gluten-free)
14 - 1 tablespoon unsalted butter, melted
15 - Fresh parsley, chopped, for garnish

# How To Make It:

01 - Preheat the oven to 400°F. Line a rimmed baking sheet with parchment paper and set aside.
02 - Using a sharp knife, carefully halve the spaghetti squash lengthwise. Scoop out and discard the seeds and stringy membranes. Place the halves cut side down on the prepared baking sheet. Roast for 35 to 40 minutes, until the flesh is fork-tender and shreds easily into strands.
03 - While the squash roasts, melt the butter in a medium saucepan over medium heat. Sprinkle in the flour and whisk continuously for about 1 minute to form a smooth roux and cook off the raw flour taste.
04 - Gradually pour in the whole milk, whisking constantly to prevent lumps from forming. Stir in the Dijon mustard, garlic powder, onion powder, salt, and black pepper. Continue cooking, stirring frequently, until the sauce thickens enough to coat the back of a spoon, about 3 to 4 minutes.
05 - Remove the saucepan from the heat. Add the shredded cheddar and Gruyère cheeses, stirring until fully melted and the sauce is silky smooth.
06 - Once the squash is cool enough to handle, use a fork to rake the flesh into long spaghetti-like strands, working from edge to center. Discard the empty skins.
07 - Add the shredded squash strands directly into the cheese sauce, tossing gently until every strand is evenly coated. Transfer the mixture to a lightly greased 9×13-inch baking dish, spreading it into an even layer.
08 - In a small bowl, combine the gluten-free breadcrumbs, grated Parmesan, and melted butter. Mix until the crumbs are evenly moistened, then sprinkle the mixture uniformly over the squash casserole.
09 - Bake at 400°F for 10 minutes, or until the topping is golden brown and the edges are bubbling. Let rest for 5 minutes before serving.
10 - Scatter chopped fresh parsley over the top and serve hot directly from the baking dish.

# Expert Suggestions:

01 -
  • You get all the cheesy, saucy satisfaction of mac and cheese without the carb coma that follows.
  • The squash strands actually hold onto the cheese sauce better than regular pasta sometimes does, which was a happy accident I discovered early on.
02 -
  • Overcooking the squash is the number one mistake because it turns mushy and watery instead of holding those distinct, satisfying strands, so check it at 35 minutes rather than guessing.
  • Always remove the sauce from heat before stirring in the cheese, since direct heat causes the proteins to separate and you end up with a greasy, broken sauce instead of a silky one.
03 -
  • Let the squash rest cut side up for five minutes after roasting so excess moisture evaporates instead of watering down your carefully built cheese sauce.
  • Reserve a handful of shredded cheddar to stir in at the very end for little pockets of stretchy, unmelted cheese throughout the dish.