Spaghetti Squash Mac and Cheese

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This easy 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, low-carb, alternative everyone’s favorite classic pasta dish (mac and cheese)!

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

This recipe 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

overhead photo of the labeled ingredients in this Spaghetti Squash Mac and Cheese recipe
  • 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.
  • Olive Oil. Avocado oil is a good substitute.
  • Salted Butter. unsalted butter or ghee are good substitutes.
  • All-purpose flour. gluten-free all-purpose flour, tapioca flour and cornstarch are all great substitutes and make thsi recipe gluten-free.
  • Cheddar Cheese. Use your favorite cheese, some suggestions include: 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

We’ll walk through how to make spaghetti squash mac and cheese step-by-step, and don’t forget to watch the video.

Bake the Spaghetti Squash

The first step in this recipe is to roast the spaghetti squash. Cut each squash into two equal halves lengthwise. Since the recipe will be baked inside of the shells, it’s important to try to keep them intact and in a good shape.

Next, 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 or brush the inside of each half wiht olive oil then sprinkle the the squash with garlic powder, sea salt and pepper. (or any other spices you choose).

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  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

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).

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 Cheese

I recommend making the cheese sauce while the squash is roasting in the oven to save time, preferably in the last 10 minutes of baking.

To make the cheese sauce, start by making a roux. 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, whisking constantly. Cook the milk/roux mixture for 3 to 5 minutes, 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 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

Assemble Spaghetti Squash Mac & Cheese

Add ½ cup of the cheese sauce to each of the four spaghetti squash halves – distributing it evenly.

For the small spaghetti squashes I used (about 2 pounds each), I find  ½ cup plus 2 Tablespoons 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

Then, 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.

Next, place the cheesy spaghetti squash halves on a large baking sheet.

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 your favorite dinner recipes, salads, etc. Here are some suggestions:

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

Store/Freeze

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

Reheat in a covered baking dish in the oven set to 300 degrees Fahrenheit until warmed through.

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

Spaghetti Squash Mac & Cheese FAQs

Is Spaghetti Squash Keto? 

Spaghetti squash is very low carb.  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:
It’s 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, manganese, 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.

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

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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
Course Main Course, Side Dish
Cuisine American
Servings 8 Servings
Calories 251.3
Prep Time10 minutes
Cook Time1 hour 15 minutes
Total Time1 hour 25 minutes

Ingredients 
 

Spaghetti Squash

Cheese Sauce

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.

Assemble

  • 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.

Bake & Serve

  • Bake in the 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.
  • Olive Oil. Avocado oil is a good substitute.
  • Salted Butter. unsalted butter or ghee are good substitutes.
  • All-purpose flour. gluten-free all-purpose flour, tapioca flour and cornstarch are all great substitutes and make thsi recipe gluten-free.
  • Cheddar Cheese. Use your favorite cheese, some suggestions include: sharp cheddar, 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.
Reheat in a covered baking dish in the oven set to 300 degrees Fahrenheit until warmed through.

Nutrition

Serving: 0.5spaghetti squash | Calories: 251.3kcal | Carbohydrates: 11.4g | Protein: 12.9g | Fat: 18.1g | Saturated Fat: 11.8g | Polyunsaturated Fat: 0.2g | Monounsaturated Fat: 0.8g | Cholesterol: 59.3mg | Sodium: 396mg | Potassium: 118mg | Fiber: 1.4g | Sugar: 4.5g | Vitamin A: 700IU | Vitamin C: 5.3mg | Calcium: 378mg | Iron: 0.4mg

Nutrition information is automatically calculated, so should only be used as an approximation.

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15 Comments

  1. 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 9×13 casseroles dish for 20 minutes with some water. Makes the recipe quicker.