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    Home » Recipes » Dinner

    Mac and Cheese Spaghetti Squash

    Modified: Mar 10, 2025 · Published: Jan 7, 2021 by Tonia Larson

    This post may contain affiliate links.

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    Mac and Cheese Spaghetti Squash is the healthier version of baked macaroni and cheese. It has all of the cheesy goodness with less carbs.

    a close-up photo of the mac and cheese spaghetti squash

    One of my favorite ways to eat more vegetables is to use simple substitutes such as cauliflower rice and spaghetti squash. While the veggies may not be an exact replica of their high carb substitute, they are a great option. The whole family will love this mac and cheese spaghetti squash!

    scooping the spaghetti squash into a mixing bowl

    Start by cooking the spaghetti squash. You can find my detailed instructions on how to cook spaghetti squash here.

    Use a fork to separate the strands of spaghetti squash and transfer it to a bowl. Save the spaghetti squash halves to use as cooking dishes and serving bowls.

    adding butter to the saucepan

    Next make the cheese sauce. I adapted my cheese sauce recipe by adding more spices. Melt the butter in a saucepan over medium-low heat.

    adding flour to the mixture in the saucepan

    Add the flour to the melted butter and whisk to combine.

    stirring the ingredients for the cheese sauce

    Cook the mixture while stirring for about 2 minutes

    stirring the cheese sauce ingredients

    Slowly whisk in the milk a little at a time. Whisk until smooth before adding more. Bring the mixture to a simmer over medium-low heat, stirring often until it begins to thicken.

    adding garlic and pepper and spices to the cheese sauce

    Add the garlic powder, black pepper, salt, and ground mustard.

    adding shredded cheddar cheese to the saucepan

    Remove from heat and stir in the shredded cheddar cheese.

    mixing the cheese and squash

    Add the spaghetti squash and stir to combine.

    filling the the halves with cheese

    Cover the bottom of each spaghetti squash half with the cooked squash. Top with shredded cheddar cheese.

    Can I make this in a casserole dish instead of the squash boats?

    Yes, you can make this mac and cheese spaghetti squash in a casserole dish! Layer the spaghetti squash and cheese in a small greased casserole dish. Bake it just as you would if it were in the boats.

    adding more shredded cheddar

    Top with the remaining spaghetti squash and sprinkle with more shredded cheese.

    What kind of cheese should I use to make mac and cheese spaghetti squash?

    I used cheddar cheese for both the cheese sauce and when layering. But you could use any shredded cheese that melts well. And if you want a little extra spice, try pepper jack cheese.

    a top down photo of the baked spaghetti squash mac and cheese

    Bake the mac and cheese spaghetti squash at 350˚F for 20-25 minutes until the cheese is bubbly and just starting to brown.

    Would it work to top it with breadcrumbs?

    Yes, if you like a crunch topping on your macaroni and cheese you can definitely add it! Panko breadcrumbs are a great choice or you could use flavored breadcrumbs if you prefer.

    a close-up top down photo of the cheesy squash

    Garnish the mac and cheese spaghetti squash with a little grated parmesan and some black pepper.

    a close-up photo of the baked macaroni and cheese spaghetti squash

    What should I serve with mac and cheese spaghetti squash?

    This mac and cheese spaghetti squash could be served as a main dish with steamed broccoli and a salad on the side. Or it could be served as a side dish with oven baked chicken and a side salad.

    taking a forkful of the delicious mac and cheese

    Want more spaghetti squash recipes? Try these next:

    This Chicken Alfredo Spaghetti Squash recipe is low carb comfort food that is easy to make. Your family won’t even miss the pasta!

    Million Dollar Spaghetti Squash is a low carb recipe the whole family will love! This baked spaghetti squash casserole is pure comfort food full of flavor and cheesy goodness.

    Easy Spinach Artichoke Spaghetti Squash with chicken recipe is a delicious low carb comfort food full of veggies!

    Skip the heavy carbs and try this recipe for Spaghetti Squash with Meatballs. This healthy dinner recipe for squash boats is a great way to eat extra vegetables!

    mac and cheese spaghetti squash.

    Mac and Cheese Spaghetti Squash

    Mac and Cheese Spaghetti Squash is the healthier version of baked macaroni and cheese. It has all of the cheesy goodness with less carbs.
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    Prep Time: 15 minutes minutes
    Cook Time: 25 minutes minutes
    Total Time: 40 minutes minutes
    Servings: 4 cups
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    Equipment

    • Small Whisk
    • Calphalon Sauce Pan

    Ingredients

    • 2 1.3 lb. spaghetti squash cooked and sliced
    • ½ cup shredded cheddar cheese
    • ¼ cup grated parmesan for garnish

    Cheese Sauce

    • 2 tablespoon butter
    • 2 tablespoon all-purpose flour
    • 1 ½ cups whole milk
    • ½ teaspoon garlic powder
    • ½ teaspoon black pepper
    • ½ teaspoon salt
    • ¼ teaspoon ground mustard
    • 1 ½ cups shredded cheddar cheese

    Instructions

    • Mac and Cheese Spaghetti Squash
    • Use a fork to separate the strands of spaghetti squash and transfer it to a bowl. Set aside. Save the spaghetti squash halves to use as bowls.
    • Prepare the cheese sauce as shown below.
    • Spread a layer of spaghetti squash in the bottom of each squash half and top it with shredded cheddar cheese. Repeat with a second layer of each.
    • Bake the mac and cheese spaghetti squash at 350˚F for 20-25 minutes until the cheese is bubbly and just starting to brown.
    • Cheese Sauce
    • Melt the butter in a saucepan over medium-low heat.
    • Whisk in the flour and cook while stirring for 2 minutes.
    • Slowly whisk in the milk a little at a time. Whisk until smooth before adding more.
    • Bring the mixture to a simmer over medium-low heat, stirring often until it begins to thicken.
    • Whisk in the garlic powder, black pepper, salt, and ground mustard.
    • Remove from heat and add the shredded cheddar cheese. Stir until smooth.

    Video

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    Notes

    Storage:

    Place in an airtight container and store in the refrigerator for up to 3 days.

    Nutrition

    Serving: 0.5cup | Calories: 528kcal | Carbohydrates: 43g | Protein: 22g | Fat: 32g | Saturated Fat: 18g | Polyunsaturated Fat: 2g | Monounsaturated Fat: 7g | Trans Fat: 0.2g | Cholesterol: 88mg | Sodium: 932mg | Potassium: 728mg | Fiber: 7g | Sugar: 18g | Vitamin A: 1524IU | Vitamin C: 10mg | Calcium: 682mg | Iron: 2mg
    Course: Dinner
    Cuisine: American
    Author: Tonia Larson

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    About Tonia Larson

    Hi! I’m Tonia, the owner and recipe creator at The Gunny Sack, where I’ve shared easy recipes for busy people for 14+ years! My family-friendly meals, easy side dishes, and delicious desserts include mouthwatering photos, dynamic videos, and step-by-step instructions to help you cook at home.

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    Tonia Larson from The Gunny Sack.

    Hi, I'm Tonia! Welcome to The Gunny Sack, where I’ve shared easy recipes for busy people for 14+ years! Meet Tonia Larson →

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