This post may include affiliate links; see our disclosure policy.
This spaghetti squash mac and cheese is a delicious, cozy vegetarian main dish that substitutes spaghetti squash for noodles!

This new recipe is a spaghetti squash mac and cheese, just as comforting and homey as it sounds! This recipe works as a main dish or a side!
For me, it’s a main dish: I could see it as a Thanksgiving recipe or a Meatless Monday entree! Or, you can pair it with a few vegetable sides like a crisp salad or roasted Brussels sprouts.
Why to make spaghetti squash mac and cheese
This new recipe is a spaghetti squash mac and cheese, just as comforting and homey as it sounds. It’s our new favorite way to sneak the nutrients of squash into a naturally gluten-free take on the traditional pasta.
Here we’ve even saved the shell to use as a serving dish. The spaghetti squash noodles are mixed with a creamy cheesy Béchamel sauce featuring Gruyere cheese. The Gruyere adds a bit of sophistication to the dish, along with a pinch of nutmeg and a dash of white wine vinegar.

Tips for cooking spaghetti squash
Roasting spaghetti squash transforms its insides into long, slender “noodles,” which is an easy way to cook it.
But did you know you can cook spaghetti squash in an Instant Pot? A pressure cooker only fits one squash, so it would work for half of this recipe (and serve it on a plate instead of in the squash). Go to Instant Pot Spaghetti Squash.

More spaghetti squash recipes
Spaghetti squash has a huge fan base! Here are all our spaghetti squash recipes:
- Spaghetti Squash with Pesto is a fantastic easy side dish.
- Spaghetti Squash Lasagna is a deliciously satisfying no noodle spin on the classic!
- Spaghetti Squash Spaghetti pairs the “noodles” with marinara and Parmesan.
- Spaghetti Squash Casserole turns it into an Italian style casserole with cheese and pesto!
- Spaghetti Squash Pad Thai is a fan favorite! It always gets rave reviews.
- Roasted Spaghetti Squash shows how to roast spaghetti squash: the right way.
- Instant Pot Spaghetti Squash is done in less than 30 minutes. Life changing!

Dietary notes
This recipe is vegetarian and gluten-free.
Spaghetti Squash Mac and Cheese
This spaghetti squash mac and cheese is a delicious, cozy vegetarian main dish that substitutes spaghetti squash for noodles!
- Prep Time: 1 hour
- Cook Time: 15 mins
- Total Time: 1 hour 15 mins
- Yield: 4 as a main; 8 as a side 1x
- Category: Main Dish
- Method: Baked
- Cuisine: American
Ingredients
- 2 large spaghetti squash (around 5 pounds)
- 6 ounces gruyere cheese (about 2 cups shredded; you also can use Jarlsberg, or a mix of Gruyere and Cheddar)
- 2 tablespoons unsalted butter
- 2 tablespoons cornstarch
- 2 cups 2% milk
- 1 ½ teaspoons kosher salt, divided
- ¼ teaspoon ground nutmeg
- Freshly ground black pepper
- 1 teaspoon white wine vinegar
- Paprika, for garnish
- Finely chopped Italian flat leaf parsley, for garnish
Instructions
- Preheat the oven to 400F.
- Using a large, sharp knife, cut the spaghetti squash in half. Scrape out the seeds using a spoon and sprinkle the cut sides with olive oil. Place the squash cut side down on a baking sheet and roast until tender and easily pierced with a knife, about 30 to 45 minutes depending on the size of the squash (check at 30 minutes regardless). When the squash is done, use a fork to carefully scrape out the flesh of each half into “noodles”, taking care to keep the squash shell intact. Place the noodles in a colander or strainer and drain for 10 minutes to remove the extra moisture. Save the squash shells for serving.
- In a medium saucepan, heat the butter over medium-low heat until melted. Add the cornstarch and stir until smooth. Over medium heat, cook until the mixture turns a light, golden sandy color, about 2 to 3 minutes.
- Meanwhile, heat the milk until hot (microwave in a glass measuring cup, or heat in another pan on the stove). Gradually add the hot milk to the butter mixture, whisking continuously until very smooth. The first addition of milk will cause the mixture to become chunky, keep whisking and adding milk until it becomes smooth. Bring to a boil and cook 3 to 5 minutes until very thick, whisking frequently. Remove from the heat and stir in 1 teaspoon kosher salt, nutmeg and several grinds black pepper. Stir in 1 ⅓ cups cheese until it melts, then add the white wine vinegar and remove from the heat.
- Add the drained squash into the pan, then mix it with the cheese sauce and ½ teaspoon kosher salt. Taste and add additional salt if desired depending on the size of the squash. Pour the mixture back into the squash shells, dividing the mixture equally among the shells. Sprinkle each squash with the remaining cheese, then with a dusting of paprika. Bake until cheese melts, about 10 minutes.
- To serve, sprinkle with chopped parsley and serve warm.
Looking for vegetarian dinner recipes?
Are you looking for cozy vegetarian dinner recipes? Here are a few you should try:



Absolutely delightful and delicious. I could tell from reading the recipe it was going to be tasty but it was even better then I expected. The biggest complement is that my 17 yr old wanted leftovers for his school lunch the next day. I’ll be sure to try pass the link on and try more of your recipes
We love to hear that! Thanks for making.
This dish was delicious I made it twice and it was a big hit, even my niece who is a 2 yr old picky eater loved it. It did taste better the next day (not sure why)
Hooray, we’re so glad! Some recipes can be better with time so the flavors soak in; glad to hear that this one ages well! (And some don’t taste better the next day, even when it seems like that they will!)
Thanks for the recipe. I was looking for other ideas for butternut squash instead of just soups. I’ll have to figure out how to make this dairy free.
If you try some substitutes, let me know! We’d be interested in what you find works here.
Awesome! Thanks for a great recipe.
I made this! I’ve never made spaghetti squash before, but it was great, and the cheese sauce is so yummy I want to put it on everything!
Oh I’m SO so glad to hear that! Yes, when I first tasted the sauce I had the same reaction :) THANKS for making it!
I love spaghetti squash recipes. My dad, who doesn’t like pasta, loved a recipe I made. I do plan on trying this one.
This one looks like I need to make it ASAP, it’s lovely! Thanks for sharing, Sonja!
We hope you like it! Thanks for the kind comment!
This looks delicious! I will definitely be making it. I would love to see more spaghetti squash recipes. I stock up on winter squash each fall from a local farm. Thirty-seven pounds this year, mostly all for me!
Ooo, wow, that’s a lot of squash! Our other spaghetti squash recipe is a fan favorite: https://www.acouplecooks.com/spaghetti-squash-pad-thai/ However, we somehow have only made 2 recipes with spaghetti squash in the 7 years of our website. Time to remedy that!