Twice-Baked Spaghetti Squash and Cheese

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

While my love for pasta is strong and unwavering, sometimes what you’re really craving is more veggies. And using roasted spaghetti squash in place of pasta in this recipe is a satisfying way to add more vegetables to a meal without sacrificing any flavor.

This twice baked spaghetti squash is so creamy and cheesy, with great flavor from the roasted spaghetti squash and a nice crunch from a topping of toasted breadcrumbs. And it works as both as side dish or a main dish!

“Love this recipe! I have made it a couple of times before and will be making it again tonight but adding some shrimp and maybe some spinach!⭐⭐⭐⭐⭐” —from reader Ashlee

Table of Contents

• What is twice baked spaghetti squash?
• Ingredients you'll need
• Tip: How to cut spaghetti squash
• 3 ways to cook spaghetti squash
• Add the creamiest cheese sauce & bake
• More veggie-full recipe to love

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 a homemade creamy cheese sauce and bake it again until it’s hot and bubbly.

Ingredients you’ll need

• Spaghetti squash (you’ll need 2, medium-sized)
• Salted butter and all-purpose flour make up a roux that forms the base of the sauce
• Mustard powder, salt and pepper add flavor
• Milk (I like to use 2%)
• Sharp cheddar cheese (shred your own cheese for the best texture)
• Panko breadcrumbs or traditional breadcrumbs, mixed with more butter for the topping

Tip: 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 (see this instructional video for a visual):

1. Use a sharp knife(very important!) to cut off the end with the stem so you have a flat edge.
2. Place the flat edge down flat on the cutting board .
3. Slice the squash in half from top to bottom. A serrated knife is helpful to saw through the tough exterior of the squash, but a sharp chefs knife will work too.

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

3 ways to cook spaghetti squash

Roast in the oven: (My preferred method, I just think it tastes the best this way.) Simply drizzle with olive oil and season with salt and pepper, then roast cut-side down on a lined sheet pan at 375ºF until tender (about 45-60 minutes).

Cook in the instant pot: (The quickest way to cook spaghetti squash!) Depending on size, 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.

Cook in the microwave: (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).

Add the creamiest cheese sauce & bake

There’s nothing cozier than a homemade cheese sauce, and this is easily my favorite part of this dish! 

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 to toast the breadcrumbs, this twice baked spaghetti squash is ready to enjoy!

More veggie-full recipe to love

• Butternut Squash, Mushroom, and Poblano Enchiladas
• Coconut Rice Veggie Bowls
• Roasted Vegetable Asiago Fettuccine Alfredo
• Mushroom Ragu with Cheesy Polenta

This recipe was originally published February 2015.