• Skip to primary navigation
  • Skip to main content
  • Skip to primary sidebar
  • Home
  • About
    • Contact
    • Privacy Policy
    • Work With Me
  • Recipe Index
  • Moments
    • Pregnancy/Baby
      • Baby Registry List
      • Thriving Postpartum: What to Expect & Postpartum Essentials for Mom
  • Shop
    • Best Kitchen Gifts
    • Baby Registry List
    • Kitchen Tools (Must Haves)
    • Pantry Staples (Baking & Cooking)
    • Food Photography Essentials
  • Instagram
JoyFoodSunshine
menu icon
go to homepage
search icon
Homepage link
  • Home
  • Recipe Index
  • About Laura
  • Contact
    • Facebook
    • Instagram
    • Pinterest
    • RSS
    • Twitter
    • YouTube
  • Never Miss a Recipe

  • ×

    Home » Spaghetti Squash Mac and Cheese

    Spaghetti Squash Mac and Cheese

    Published: Jan 10, 2019 · Modified: Nov 15, 2021 by Laura · This post may contain affiliate links.

    Jump to Recipe

    This easy & healthy Spaghetti Squash Mac and Cheese Recipe is low-carb and keto-friendly! It's creamy, cheesy and delicious.

    Front view of a hand holding a fork pulling a bite of Spaghetti Squash Mac and Cheese out of the shell

    I created this Spaghetti Squash Mac and Cheese as a satisfying, but healthier, alternative everyone's favorite classic pasta dish (mac and cheese)!

    This spaghetti squash mac and cheese recipe is low-carb and is a healthy & delicious gluten-free dinner, side dish or meal prep idea! It's perfect to reheat for lunch with a salad or side of veggies!

    This spaghetti squash mac and cheese is also keto-friendly which is great if you are craving mac and cheese but need to eat a low-carb diet.

    Up close overhead view of a fork taking a bite of Spaghetti Squash Mac and Cheese in the shell

    Spaghetti Squash Mac & Cheese: Ingredients & Substitutions

    Let's take a minute and chat about the ingredients in this Spaghetti Squash Mac and Cheese recipe, as well as possible substitutions!

    • Spaghetti Squash. I do not recommend making substituions for the spaghetti squash in this recipe! The only thing that might vary in regards to the squash is the size. You could use one very large 4 lb. squash and only cut it into two halves instead of four if that is what you can find! Just note you will have to adjust the roasting time accordingly.
    • Olive Oil. Any neutral oil works perfectly in this recipe. The purpose of the oil is to help the salt/pepper/spices adhere to the squash before roasting. I recommend olive oil or avocado oil.
    • Butter. The butter adds such a great flavor and texture to the cheese sauce, that I cannot (in good conscience) suggest substituting it for anything else, except maybe ghee.
    • All-purpose flour. There are actually lots of different substitutions that can be made for the all-purpose flour in this recipe. I have used gluten-free all-purpose flour, tapioca flour and cornstarch with great success. Choose whichever variety best fits your dietary needs.
    • Cheddar Cheese. The sharpness and flavor of the cheese is totally up to you to choose! We like extra sharp cheddar in our house, as well as gouda, gruyere, etc.
    overhead view of Spaghetti Squash Mac and Cheese on a plate with a fork taking a bite

    How to make Spaghetti Squash Mac and Cheese

    I made sure to thoroughly document exactly how to make this baked Spaghetti Squash Mac and Cheese recipe for you! It may seem like a lot of steps, but it's really easy! Here is an overview of the process:

    1. Roast & shred the spaghetti squash
    2. Make the cheese sauce & add it to the shredded squash!
    3. Top with more cheese, bake and enjoy!

    However, now I will break it down step-by-step to ensure your success when making this baked spaghetti squash recipe!

    Overhead view of four spaghetti squash halves filled with Spaghetti Squash Mac and Cheese and sprinkled with parsley after baking, one has a fork in it

    Roast the spaghetti squash

    Cut the squash in half

    The first step in this recipe is to roast the spaghetti squash. Note: Be sure to cut the squash into two equal halves (for the sake of even baking times). Since the Spaghetti Squash Mac and Cheese will be baked inside of the shells, it's important to try to keep them intact and in a good shape!

    Remove guts/seeds

    This process is very simple! Just use a firm metal spoon or even an ice cream scooper and scrape the insides out of the squash as you would before carving a pumpkin on Halloween.

    Throw the insides/seeds away in the garbage. I don't recommend putting them down the garbage disposal, as the seeds are pretty tough!

    two overhead photos showing How to make Spaghetti Squash Mac and Cheese - roasting the spaghetti squash

    Spray the inside with oil & Spices.

    I use a spray avocado oil  for this step. However, you can also simply rub olive oil on the inside and then sprinkle the the squash with garlic salt (or any other spices you choose). Please don't skip this step. It adds so much flavor to the squash as it roasts!

    Place the spaghetti squash cut-side down in a rimmed baking pan and fill the pan with boiling water. 

    After coating the inside with oil & spices, flip the spaghetti squash halves over so they are face-down in a large baking sheet.

    Pour boiling water into the pan to fill it so that about ¼ to ½" of the bottom of the spaghetti squash is submerged in water. Baking the Spaghetti Squash in water helps make it moist and easy to shred.

    two overhead photos showing How to make Spaghetti Squash Mac and Cheese - roasting the squash

    Cover with foil and bake

    Next, cover the baking sheet with foil (to retain the water as long as possible) and place in the preheated oven. Roast for 45-60 minutes (depending on the size of your squash).

    How can you tell when spaghetti squash is cooked? 

    You will know the spaghetti squash is cooked when you can easily press the top down with your hand and it stays depressed.

    front view of hands placing aluminum foil over a baking sheet before placing it in the oven to make Spaghetti Squash Mac and Cheese

    Shred the Spaghetti Squash

    Next, very carefully take a fork and run it lengthwise across the spaghetti squash until all the insides are shredded (as pictured below).

    Since the cheese sauce will be mixed with the squash inside of the shells and baked, it's important to shred the squash very carefully and gently to avoid breaking the shells!

    two photos showing how to make spaghetti squash mac and cheese - shredding the squash in the shells

    Make the sauce

    I recommend making the cheese sauce while the squash is roasting in the oven to save time! Then keeping it covered with a lid until you're ready to use it.

    To make the cheese sauce, start by making a roux. To do this, melt the butter, mix the dry ingredients together and then add them to the butter in the saucepan.

    two photos showing how to make spaghetti squash mac and cheese sauce

    Use a wire whisk and whisk until the dry ingredients are incorporated into the melted butter. Then cook for about 1 minute, or until bubbles begin to form in the mixture (see picture below on the right hand side).

    two photos showing how to make spaghetti squash mac and cheese sauce

    Next, pour the milk into the roux in the saucepan while whisking constantly. Cook the milk/roux mixture for about 5 minutes, or until it becomes thick.

    Once the milk mixture is thick, add the shredded cheese and turn off the heat (or at least reduce it to low). Whisk until the cheese is completely melted and the sauce is smooth.

    two photos showing how to make spaghetti squash mac and cheese sauce

    The mixture (before the cheese is added) will release steam as it cooks. This is part of the thickening process (water evaporating) and is normal and critical to a thick melty cheese sauce!

    The cheese sauce will also thicken as it cools, which is something to be aware of if you prepare it long before the spaghetti squash has finished roasting. If it becomes too thick as it sits, simply re-warm it on the burner over low heat!

    Front view of steam coming out of a pot as hands whisk the ingredients in the cheese sauce for this Spaghetti Squash Mac and Cheese recipe

    Putting it together

    Add ½ cup of the cheese sauce to each of the four spaghetti squash halves. Then go back and add 1-2 TBS more sauce to each squash.

    For the small spaghetti squashes I used (about 2 LBS each), I found ½ cup plus 2 TBS sauce was the perfect amount to fill each squash-half and use all the sauce. However this amount will vary depending on the size of your squash.

    Front view of a measuring cup pouring cheese sauce into a shredded spaghetti squash half in the making of this Spaghetti Squash Mac and Cheese recipe

    Use a fork to gently incorporate the cheese sauce into the shredded spaghetti squash. As you can see, the mixture should be thick and not at all runny.

    Place the cheesy spaghetti squash halves on a large baking sheet to prepare to finish this baked Spaghetti Squash Mac and Cheese!

    two overhead photos showing how to make spaghetti squash mac and cheese

    Sprinkle some more cheese on top of each squash and then bake in the preheated oven until the cheese is melted.

    The longer you bake the Spaghetti Squash Mac and Cheese recipe, the firmer the cheese on top will be. Use your discretion and bake as long as it takes to reach the texture you would enjoy the most!

    two overhead photos showing how to make spaghetti squash mac and cheese

    Serve

    Serve plain or with a garnish of fresh herbs or parmesan cheese alongside some of these dishes.

    • On the side of this balsamic pot roast (a family favorite)!
    • Serve it with a salad like this kale salad or brussel sprouts salad.
    • For a truly kid-friendly dinner, serve it with these healthy Sloppy Joes!
    • Add some balsamic roasted veggetables!
    • Serve it alongside this avocado chicken salad
    • This oven-roasted broccoli pairs perfectly with this spaghetti squash mac and cheese!
    • Balsamic roasted brussels sprouts taste amazing with this dish!

    Store/freeze

    Store in an airtight container in the refrigerator for 3-5 days, or in the freezer for up to 1 month.

    Front view of a hand holding a fork taking a bite of Spaghetti Squash Mac and Cheese out of one of four halves in a baking sheet

    FAQs about Spaghetti Squash Mac and Cheese!

    Recipe FAQs

    Is Spaghetti Squash Keto? 

    Spaghetti squash is very low carb, but it is not carb-free. ½ cup of spaghetti squash contains roughly 20 calories and 5 g of carbs. So while it fits in the keto diet, you still need to watch your portion size!

    How many carbs are in baked spaghetti squash? 

    ½ cup baked spaghetti squash has 20 calories and 5 g of carbs.

    Is Spaghetti Squash better for you than pasta? 

    I am a proponent of everything in moderation. I would not say that pasta is "bad for you!" However, spaghetti squash definitely has a few health benefits over regular pasta. Spaghetti squash is...
    Lower in calories (only 40 calories in 1 cup as opposed to over 200 in most cases for pasta)
    Relatively high in fiber (1 cup has 2.2 g of fiber).
    Contains many vitamins & minerals (vitamin C, potassium, iron, Vitamin B6, magnanese, etc.)
    Very low in carbs (only 5 g in ½ cup).

    How do I make this Spaghetti Squash Mac & Cheese Keto?

    Disclaimer: I am not an expert on the Keto diet, but from what I understand the main concern is consuming less than 30 g of carbs per day.
    The recipe calls for whole milk and there is 11 g of carbs per serving (without making a low-carb substitute for the flour). You can use heavy cream instead of whole milk, which has an even lower carb count and tapioca flour instead of all-purpose flour...and get a net carb count of 9.4 g per serving.
    You can also try substituting unsweetened coconut milk, almond milk, pea milk, hemp milk or flax milk, but be aware that the flavor and texture of those milks will change the final flavor of the dish!

    Front view of a half of a spaghetti squash with a fork in it and Spaghetti Squash Mac and Cheese sprinkled with parsley

    If you make and love our recipes, it would mean so much to me if you would leave a comment and rating! And don't forget to follow along with us on Instagram, Pinterest, Facebook, and Youtube - be sure to tag @joyfoodsunshine and use the hashtag #joyfoodsunshine so we can your creations!

    Spaghetti Squash Mac and Cheese

    Laura
    This easy & healthy Spaghetti Squash Mac and Cheese Recipe is low-carb and keto-friendly! It's creamy, cheesy and delicious.
    5 from 16 votes
    Print Recipe Pin Recipe Save Recipe Saved!
    Prep Time 10 mins
    Cook Time 1 hr 15 mins
    Total Time 1 hr 25 mins
    Course Main Course, Side Dish
    Cuisine American
    Servings 8 Servings
    Calories 251.3 kcal

    Equipment

    • measuring spoons
    • measuring cups
    • whisk
    • 5 Quart Sauce Pan
    • baking sheet

    Ingredients
     
     

    Spaghetti Squash:

    • 2 small/medium spaghetti squash about 2 lbs each
    • 1 TBS olive oil
    • ½ tsp garlic salt (or to taste)
    • ¼ tsp freshly ground black pepper (or to taste)

    Cheese Sauce:

    • 2 TBS butter
    • 2 TBS all-purpose flour* (or gluten-free all-purpose flour, tapioca flour or cornstarch)
    • ½ tsp sea salt
    • ¼ tsp garlic powder
    • 1 ½ cups  whole milk
    • 2 ½ cups sharp cheddar cheese divided.
    Prevent your screen from going dark

    Instructions
     

    Roast the spaghetti squash:

    • Preheat oven to 400 degrees F.
    • Cut both spaghetti squash in half and remove the seeds (scoop them out with a metal spoon).
    • Brush the inside with olive oil (or spray with an olive oil spray) and sprinkle with sea salt and pepper.
    • Place cut-side down in a baking dish.
    • Fill baking dish ¼” with water.
    • Cover baking dish with aluminum foil.
    • Bake in the preheated oven for 45-60 minutes or until the squash is soft to the touch (it will compress down when pushed lightly).
    • Remove from the oven and turn the cut-side to the top.
    • Let cool.
    • Use a fork to shred the spaghetti squash, being careful not to poke holes in the shell.
    • Leave shredded spaghetti squash in the shell while you make the cheese sauce.

    Make the cheese sauce:

    • Preheat oven to 375 degrees F.
    • In a small bowl, combine flour sea salt and garlic powder. Set aside.
    • Melt butter in a medium saucepan over medium heat.
    • Add dry ingredients and whisk to combine.
    • Whisk constantly until ingredients just start to brown (about 1-2 minutes).
    • Add milk and whisk until mixture is smooth.
    • Continue cooking over medium-high heat until the mixture comes to a boil and starts to thicken (about 3-5 minutes).
    • Once mixture is thick, add 2 cups of shredded cheese and whisk until the cheese is completely melted.
    • Once cheese sauce is smooth, remove the saucepan from the heat.

    Putting it together:

    • Distribute cheese sauce evenly among the four halves of shredded spaghetti squash (with the size squashes I had, I used about ½ cup plus 2 TBS of cheese sauce for each of the four halves).
    • Use a fork to gently stir the cheese sauce into each half of shredded spaghetti squash.
    • Once the sauce is evenly distributed in the squash, use the fork or a spatula to smooth out the surface of each squash half.
    • Top with remaining ½ cup of cheese and bake in preheated oven for 15 minutes, or until the cheese on the top is melted and lightly brown.
    • Serve warm!

    Video

    Notes

    *for an even lower carb count than listed in the nutritional information (which was calculated using all-purpose flour), use tapioca starch! 
    Ingredient substitutions
    • Spaghetti Squash. I do not recommend making substituions for the spaghetti squash in this recipe! The only thing that might vary in regards to the squash is the size. You could use one very large 4 lb. squash and only cut it into two halves instead of four if that is what you can find! Just note you will have to adjust the roasting time accordingly.
    • Olive Oil. Any neutral oil works perfectly in this recipe. The purpose of the oil is to help the salt/pepper/spices adhere to the squash before roasting. I recommend olive oil or avocado oil.
    • Butter. The butter adds such a great flavor and texture to the cheese sauce, that I cannot (in good conscience) suggest substituting it for anything else, except maybe ghee.
    • All-purpose flour. There are actually lots of different substitutions that can be made for the all-purpose flour in this recipe. I have used gluten-free all-purpose flour, tapioca flour and cornstarch with great success. Choose whichever variety best fits your dietary needs.
    • Cheddar Cheese. The sharpness and flavor of the cheese is totally up to you to choose! We like extra sharp cheddar in our house, as well as gouda, gruyere, etc.

    Store/freeze

    Store in an airtight container in the refrigerator for 3-5 days, or in the freezer for up to 1 month.

    Nutrition

    Serving: 0.5spaghetti squashCalories: 251.3kcalCarbohydrates: 11.4gProtein: 12.9gFat: 18.1gSaturated Fat: 11.8gPolyunsaturated Fat: 0.2gMonounsaturated Fat: 0.8gCholesterol: 59.3mgSodium: 396mgPotassium: 118mgFiber: 1.4gSugar: 4.5gVitamin A: 700IUVitamin C: 5.3mgCalcium: 378mgIron: 0.4mg
    Tried this recipe?Let us know how it was!

    More delicious mac and cheese recipes: 

    • This homemade mac and cheese made on the stovetop is our favorite!
    • This baked mac and cheese can be made gluten-free!
    • Add some nutrition and make this Vegetable Mac and Cheese!

    This post contains affiliate links, which means that if you purchase a product through a link you clicked on here, I receive a portion of the sale. Thank you for supporting JoyFoodSunshine!

    « Apple Cider Vinaigrette
    Healthy Strawberry Banana Smoothie »

    Did you make this recipe?

    Leave a comment and review below, then take a picture and tag @joyfoodsunshine #joyfoodsunshine on Instagram so I can see it! Sign up here to receive weekly e-mails!

    Reader Interactions

    Comments

    1. Lindsey

      December 05, 2021 at 6:00 pm

      5 stars
      A winter staple in my home. I use 2% milk and mild cheddar cheese and it still comes out super rich and tasty. Instead of baking the squash the first time, I microwave the halves in a 9x13 casseroles dish for 20 minutes with some water. Makes the recipe quicker.

      Reply
    2. Eloise

      April 13, 2021 at 9:33 pm

      5 stars
      Tried this dish today and it was AMAZING! We are pretty strict about carbs though, so instead of using any flour we created a keto “roux” by mixing cream cheese, butter, and heavy cream together with the cheese. It came out sooooo good. Definitely will be making this again soon.

      Reply
    3. Tricia

      March 04, 2021 at 12:39 pm

      being lactose free my self , will almond milk just as well. making this tonight. thank you

      Reply
    « Older Comments

    Leave a Reply Cancel reply

    Your email address will not be published. Required fields are marked *

    Recipe Rating




    This site uses Akismet to reduce spam. Learn how your comment data is processed.

    Primary Sidebar

    Search

    About Laura

    I’m Laura, a former chemistry teacher turned homeschooling mom of six beautiful babies! I create simple and delicious recipes that are tested and perfected to make cooking and baking joyful and fun!

    Click here to read more >>

    • Facebook
    • Instagram
    • Pinterest
    • RSS Feed
    • Twitter
    • YouTube

    Most Popular Recipes

    • The Best Chocolate Chip Cookie Recipe Ever
    • Best Cinnamon Rolls Recipe (Better than Cinnabon)
    • Easy Homemade Pizza Dough Recipe
    • Easy Dutch Oven No Knead Bread
    • Easy Homemade Pizza Sauce Recipe (5- Minutes)
    • Asian Chicken Lettuce Wraps
      Asian Chicken Lettuce Wraps (Better than P.F. Chang's)!

    Trending now

    • Blueberry Baked Oatmeal Recipe
    • Healthy Pineapple Carrot Cake
    • The Best Banana Cake Recipe
    • Egg Casserole (Egg Bake)
    • Baked French Toast Casserole
    • Best Carrot Cake Recipe
      Best Carrot Cake Recipe

    Footer

    ↑ back to top

    Joy Food Sunshine Logo
    • Facebook
    • Instagram
    • Pinterest
    • RSS Feed
    • Twitter
    • YouTube

    Never Miss a Recipe

    53963 shares
    • 5064