Twice-Baked Spaghetti Squash and Cheese

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It’s just like the classic baked macaroni and cheese, but without the noodles! And you won’t even miss ’em, I promise.

Twice Baked Spaghetti Squash and Cheese |

While my love for pasta is strong and unwavering, I have wholeheartedly jumped on the spaghetti-squash-in-place-of-actual-pasta bandwagon. Sometimes you just have to swap out the carbs for some veggies.

It makes for more calorie wiggle room for cookies, which is such a nice bonus.

So every so often I “healthify” one of our regular pasta dishes with spaghetti squash, and I have yet to hear complaints from my husband or picky toddler. My latest experiment? This twice baked spaghetti squash and cheese. And we gobbled it up! 

Twice Baked Spaghetti Squash and Cheese |

All I did was take a classic mac and cheese recipe and sub baked spaghetti squash for the noodles. The sauce is the same, and so is the breadcrumb topping. While I admit it’s not as indulgent as the original, you really won’t miss the pasta. It’s still creamy, cheesy and cozy. All the things that macaroni and cheese should be.

You could serve this spaghetti squash and cheese as a simple (and vegetarian) dinner for two, or keep it as a side dish alongside a protein like pork or chicken.

And a quick note, because I’ve gotten a lot of comments on this— it’s not a “low carb” dish! Definitely a little lower in carbs since I’ve nixed the pasta, but not “low carb”.

Twice Baked Spaghetti Squash and Cheese |

baking tip:The secret to the creamiest cheese sauce

This dish, and most mac and cheese recipes, start with a roux-based sauce made from whisking milk into a flour mixture.

The wrong way to do it: Dump all the milk in quickly, whisking a little or not at all. This will result in a lumpy sauce that won’t thicken properly.

The right way to do it: Add a little milk to the pan to start and whisk until it is fully incorporated into the flour. Do this a few more times until the mixture starts to look like a sauce, whisking until there are not lumps. Slowly pour the rest of the milk while whisking constantly. It will take more time, but you’ll end up with a smooth and creamy sauce.

How to save a lumpy sauce: Mix in a blender until smooth. Return to heat and stir until thickened.

Twice Baked Spaghetti Squash and Cheese |

Watch the video

Twice Baked Spaghetti Squash and Cheese

Just like traditional baked mac and cheese, but without the noodles! Makes a great light meal or side dish.


  • 2 medium spaghetti squash, halved lengthwise and seeds removed
  • 5 tablespoons (70 grams) butter, divided
  • 1/2 cup (70 grams) onion, finely chopped
  • 2 tablespoons all-purpose flour
  • 1 teaspoon mustard powder
  • 2 cups (475 ml) milk (can use skim, 1%, 2% or whole)
  • 8 ounces (225 grams) sharp cheddar cheese, shredded
  • 1 teaspoon salt
  • 1/4 teaspoon ground pepper
  • 1 cup (50 grams) panko bread crumbs


  1. Preheat oven to 375 degrees F. Line a sheet pan with parchment paper. Place spaghetti squash on parchment, cut side-up and sprinkle with salt. Cover with foil and bake until fork tender, about 1 hour.
  2. Let spaghetti squash sit a few minutes until cool enough to handle, then shred flesh with a fork. Transfer squash flesh to a large bowl and set aside. Reduce oven temperature to 350 degrees F.
  3. In a large skillet, melt 2 tablespoons of the butter. Add the onion and cool until translucent, about 5 minutes. Add flour and mustard powder and stir with a whisk until it makes a thick paste. Slowly pour the milk into the pan while whisking constantly. Bring to a boil, then cook for a few minutes until thickened, stirring frequently. Add the cheddar cheese, salt and pepper and stir until smooth.
  4. Pour the cheese mixture into the large bowl with the spaghetti squash and toss until combined. Divide evenly into the 4 squash skins.
  5. Melt the remaining 3 tablespoons of butter. Add the panko bread crumbs and stir until all the bread crumbs are moistened. Sprinkle on top of the spaghetti squash.
  6. Bake until filling is bubbling and topping is browned, about 30 minutes. Serve immediately.

Have you tried this recipe?

I’d love to hear about it! Leave a comment below, send me an email, or take a photo and tag it on instagram with #completelydelicious.