by Olena

Spaghetti Squash Mac and Cheese

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Olena Osipov
5 from 4 votes

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Spaghetti Squash Mac and Cheese is traditional comfort food without the extra calories made with vegetables, a bit of butter or coconut oil and only a cup of cheese.

Looking for more spaghetti squash recipes? Try chicken alfredo spaghetti squash boats and spaghetti squash casserole.

Spaghetti Squash Mac and Cheese

Spaghetti Squash Mac and Cheese

Let’s be clear from the very beginning – this spaghetti squash mac and cheese recipe won’t replace pasta. But it will satisfy your craving for a bowl of comforting pasta and cheese without all of the carbs!

Spaghetti squash mac and cheese is a healthier version of traditional mac and cheese and it is so easy to make!

The sauce is made lighter by using butter and whole wheat flour, cutting back the amount of cheese and eliminating the heavy cream. And the taste is incredible!

This healthy squash mac and cheese recipe is perfect for a low carb lunch, dinner or even a side dish!

Spaghetti Squash Mac and Cheese in skillet

Ingredients for Spaghetti Squash Mac and Cheese

  • Spaghetti squash: Choose a light coloured squash as it is much easier to cut open than the bright yellow ones.
  • Butter or coconut oil
  • Whole wheat or spelt flour: If you are gluten intolerant/sensitive you probably know better than me how to replace flour with cornstarch, arrowroot powder or xanthan gum. I haven’t tested a gluten free version of this recipe myself.
  • Milk of your choice: I use unsweetened almond milk.
  • Seasonings: Salt, pepper, garlic or onion powder and red pepper flakes.
  • Cheese: Any hard cheese. I use mozzarella.

How to Make Spaghetti Squash Mac and Cheese

There is a full recipe card below.

  • Prep and cook squash: Wash squash, cut in half lengthwise and scoop out the seeds. On a parchment paper lined baking sheet, place the cut side down. Bake for 40-50 minutes at 375 degrees F. Be careful not to overcook it as it will become watery, and mushy. Once cooled, separate strands with a fork. You can also cook spaghetti squash in Instant Pot – so easy!

scooping out spaghetti squash

  • Make cheese sauce: First, preheat medium pot or dutch oven and melt butter/oil. Then, whisk in flour until small lumps form. Keep whisking while you slowly add milk. Follow with salt, pepper, onion powder and pepper flakes. After simmering for 3-4 minutes (or until the sauce has thickened), add the cheese and stir until smooth.

mac and cheese sauce

  • Add squash to sauce: Mix spaghetti squash into the cream sauce gently with a spoon. Cover to allow the squash to warm through. Serve hot. Spaghetti Squash Mac and Cheese in bowl

How to Store Spaghetti Squash Mac and Cheese

Store: Leftovers can be stored in an airtight container for up to 3 – 4 days in the refrigerator.

Freeze: Spaghetti squash does NOT freeze well.
Spaghetti Squash Mac and Cheese

Spaghetti Squash Mac and Cheese

Spaghetti Squash Mac and Cheese is traditional comfort food without the extra calories made with vegetables, a bit of butter or coconut oil and only a cup of cheese.
5 from 4 votes
Print Save Rate
Course: Dinner
Cuisine: North American
Prep Time: 10 minutes
Cook Time: 1 hour
Total Time: 1 hour 10 minutes
Servings: 6 servings
Calories: 238kcal
Author: Olena Osipov



  • Preheat oven to 375 F degrees F and line a baking sheet with unbleached parchment paper.
  • Wash squash, cut in half lengthwise and remove seeds with a spoon. Punch randomly with a fork, place cut side down on previously prepared baking sheet and bake for 40-50 minutes.
  • Remove squash from the oven, let cool until it's safe to the touch and separate into strands with a fork. Cut into 2” strands using kitchen scissors. Set aside.
  • In the meanwhile, preheat medium pot or dutch oven on low-medium heat and melt butter or oil. Whisk in flour until small lumps form.
  • Add milk and keep whisking until smooth.
  • Add salt, onion powder and pepper; whisk and let simmer for about 3-4 minutes or until sauce has slightly thickened.
  • Add cheese and whisk again until smooth.
  • Add squash and mix gently with a spoon to combine. Cover and let squash warm through for about 5 minutes. Serve hot.

Store: Refrigerate in an airtight container for up to 3 - 4 days. Do not freeze.


    *I like both ways, depends on how much you like coconut oil.
    **I have not tried to make this recipe gluten free, so I don’t know.


    Serving: 1.5cups | Calories: 238kcal | Carbohydrates: 18g | Protein: 9g | Fat: 16g | Saturated Fat: 9g | Cholesterol: 43mg | Sodium: 520mg | Fiber: 3g | Sugar: 9g

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    19 comments on “Spaghetti Squash Mac and Cheese

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    1. Hi Olena, does baking mat work the same in this recipe as parchment paper?
      Have you tried to cook spaghetti squash in your Instant Pot instead of baking it in the oven? Is the oven baked one comes out more tasty? Thanks 🙂

      1. Hi Leto. Yes you can use baking mat. I tried in IP but it came out so watery and mushy. Needs more testing. I like baking more for now.

    2. This is an excellent basic recipe with good comfort food mouth feel. I just riffed on it adding cajun spices and cooking green beans in garlic on the side to add at the end along with the spaghetti squash. Next time, I’ll make sure to use whole milk!

    3. 5 stars
      I just made this tonight for dinner, and I made it with coconut flour, which is gluten free, and oh wow this is yummy!! My siblings are a tad picky, and they got seconds! A+ recipe, definitely keeping this on the rotation. Thank you!!

        1. Nope, not gritty at all and the sauce did thicken, but not as much as it would with wheat flour. It worked really well!

    4. I’m trying this website with my husband’s family Saturday and I look forward to trying it. I absolutely love spaghetti squash and look forward to any new recipes I find to try it! It will be a test though, his mom is a true Mac and cheese lover but we have cut out must carbs which means no more pastas for us so can’t wait to try it! Looks yummy!

    5. Hi, Just a question…why can this recipe not be frozen? Is it unsafe/unhealthy to freeze? Or will it just not taste the same after being frozen? Thank you!

      1. Hi Stefanie. Spaghetti squash mac and cheese just won’t taste good thawed. The sauce and the squash itself. Trust me. It’s like frozen potato or zucchini. I personally do not enjoy eating it thawed and I’m not picky at all. This recipe refrigerates well though for a long time.

    6. I am with you! Cooking is my favorite thing EVER. I have my squash roasting in the oven now and can’t wait to try this recipe!

    7. 5 stars
      Hi Olena! I’m a 28 year old husband and new father to an 8 month old beautiful daughter. My wife and I both work full time and the way our schedule works, I ended up taking on the cooking. I stumbled onto your website for the squash bowls, and have to say you are a genius. LITERALLY every recipe I’ve made has been a total win. My family’s eating healthier and I have a real passion to cook with excellence and with actual real food. Thanks for all the recipes and for being an inspiration!!

      1. Hi J.T. Your comment was not the one I’m used to because majority of my readers are women. So I’m super proud of you and happy to see a man who didn’t take an easy way of putting dinner on a table via processed foods. Your efforts will pay you back million times, especially through a healthy child!!! Thank you so much for your kind words – I just like to cook.:) Enjoy!

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