Twice-Baked Spaghetti Squash and Cheese

All the comfort of traditional mac and cheese, but with veggies! This twice-baked spaghetti squash and cheese is sure to become one of your favorites.

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.

So every so often I “healthify” one of our regular pasta dishes with spaghetti squash, and I have yet to hear complaints from my family. I first posted this twice baked spaghetti squash and cheese recipe in 2015 and it’s been a favorite ever since!

It’s so creamy and cheesy, with great flavor from the roasted spaghetti squash and a nice crunch from the topping of toasted breadcrumbs.

What is Twice Baked Spaghetti Squash?

It’s just like it sounds! First, roast the spaghetti squash in the oven until tender (though you can also do this step in the microwave or instant pot, see below). Then, you shred the flesh with a fork and add whatever sauces or mix-ins to the squash you want— for this recipe I’m using a cheese sauce— and bake it until it’s hot and bubbly.

It’s so good! One of the favorite comfort foods.

Ingredients need to make this Twice Baked Spaghetti Squash and Cheese

Here’s what you’ll need:

  • 2 medium-sized spaghetti squash
  • Butter
  • All-purpose flour
  • Mustard powder
  • Milk
  • Sharp cheddar cheese
  • Panko breadcrumbs

How to Cut Spaghetti Squash

We can all agree that cutting large squashes like butternut, acorn, and spaghetti squash isn’t always easy, right? This is the method that works for me:

  1. Place spaghetti squash on it’s side on a cutting board. Using a sharp knife, cut off the end with the stem so you have a flat edge.
  2. Place that flat edge flat on the cutting board so the squash is sticking up.
  3. Use a sharp knife (very important) to slice the squash in half from top to bottom. A serrated knife is helpful because it helps saw through the tough exterior of the squash, but a sharp chefs knife will work too.

This video makes it look so easy!

Once the spaghetti squash is halved, remove the seeds and pulp with a spoon and discard. Then, it’s for cooking.

How to Cook Spaghetti Squash

Roast in the oven— The most traditional way to cook spaghetti squash is to roast it in the oven. And honestly, I think the spaghetti squash tastes the best this way. Simply drizzle with olive oil and season with salt and pepper, then roast on a lined sheet pan at 375ºF until tender (about 45-60 minutes).

In the instant pot— This is definitely the quickest way to cook spaghetti squash! Though depending on the size of your squash, you may only be able to cook a few at a time. Place trivet inside your instant pot, then fill with 1 cup water and add the spaghetti squash. Set high pressure to 6 minutes and use a quick release.

In the microwave— The microwave is another great option too to cut down on time. Place spaghetti squash cut side-down into a microwave-safe dish that will fit your microwave and add 1/2 cup water. Microwave on high for about 15 minutes until fork tender (time will vary based on side of spaghetti squash).

The Creamiest Cheese Sauce

There’s nothing cozier than a homemade cheese sauce, and this is easily my favorite part of this dish! Roasted spaghetti squash is tasty on it’s own, but this cheese sauce takes it to a whole new level of flavor.

This is a simple cheese sauce that starts with a roux of butter and flour, then you add milk, cheese, mustard powder, and salt and pepper. It’s smooth, creamy, and oh so cheesy. A sprinkling of breadcrumbs is the final touch.

After another quick bake in the oven, this twice baked spaghetti squash is cheesy, cozy, and so satisfying. Serve it as a light meatless meal, or serve it as a side dish!

Other veggie-full recipe to love:

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This recipe was originally published February 2015.

Twice Baked Spaghetti Squash and Cheese

All the comfort of traditional mac and cheese, but with veggies! This twice-baked spaghetti squash and cheese is sure to become one of your favorites.
Twice Baked Spaghetti Squash and Cheese | completelydelicious.com
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5 from 1 vote

Ingredients

  • 2 medium spaghetti squash , halved lengthwise and seeds removed
  • Olive oil , for drizzling
  • 3 tablespoons butter , divided
  • 2 tablespoons all-purpose flour
  • 1 teaspoon mustard powder
  • 2 cups milk (can use skim, 1%, 2% or whole)
  • 8 ounces sharp cheddar cheese , shredded
  • 1 teaspoon salt
  • 1/4 teaspoon ground pepper
  • 1 cup panko bread crumbs

Instructions

  • Preheat oven to 375 degrees F. Line a sheet pan with parchment paper or foil.
  • Drizzle squash with olive oil and season with salt and pepper. Place cut side-down on prepared sheet pan and bake until fork tender, about 45-60 minutes.
  • Let spaghetti squash sit a few minutes until cool enough to handle, then shred flesh with a fork.
  • In a large skillet, melt 2 tablespoons of the butter. Add flour 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, mustard powder, salt and pepper and stir until smooth.
  • Add spaghetti squash and toss until combined. Divide evenly into the 4 squash skins.
  • Melt the remaining 1 tablespoon of butter. Add the panko bread crumbs and stir until all the bread crumbs are moistened. Sprinkle on top of the spaghetti squash.
  • Bake until filling is bubbling and topping is browned, about 20 minutes. Serve immediately.
NOTES:
  • To cook spaghetti squash in instant pot: Place trivet inside your instant pot, then fill with 1 cup water and add the spaghetti squash. Set high pressure to 6 minutes and use a quick release.
  • To cook spaghetti squash in the microwave: Place spaghetti squash cut side-down into a microwave-safe dish that will fit your microwave and add 1/2 cup water. Microwave on high for about 15 minutes until fork tender (time will vary based on side of spaghetti squash).

Nutrition

Calories: 604kcal, Carbohydrates: 54g, Protein: 24g, Fat: 35g, Saturated Fat: 20g, Cholesterol: 94mg, Sodium: 1253mg, Potassium: 767mg, Fiber: 8g, Sugar: 21g, Vitamin A: 1608IU, Vitamin C: 10mg, Calcium: 688mg, Iron: 3mg

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