Gluten-free butternut squash mac and cheese is perfect as an everyday fall dinner or Thanksgiving side dish. This delicious and healthy twist on a classic mac and cheese is packed with flavor and a healthy dose of vegetable.

Gluten-Free Butternut Squash Mac and Cheese

With colder weather approaching, we’re all craving classic comfort foods like stews, soups, and cheesy casseroles. There’s one that stands out as a favorite with both kids and adults alike and that’s mac and cheese—but did you know you can add some healthy goodness without losing its signature gooey, cheesy texture?

Butternut squash has a mild flavor that adds a subtle sweetness to the casserole. It’s a great addition in the fall when squashes come into season and works as both a simple weeknight dinner or a vibrant Thanksgiving side dish.

Check out my tips for making the best gluten-free butternut squash mac and cheese below.

Ingredients

• Butternut Squash: You’ll need 2 pounds to roast. When shopping, look for one that’s at least 2 ½ pounds in size because you’ll be peeling it and removing the seeds inside. 
• Gluten-Free Macaroni: It wouldn’t be mac and cheese without the mac! Choose a gluten-free version that you’ve tried before and enjoy the taste and texture of.
• Unsalted Butter: Gives the cheese sauce its rich flavor.
• Gluten-Free All-Purpose Flour: Used to thicken the sauce so it’s not runny.
• Whole Milk: Gives the sauce its creamy texture. Avoid the low-fat milks for this recipe.
• Italian Seasoning: A blend of basil, oregano, rosemary, thyme, and marjoram that adds a lovely aroma.
• Cheddar Cheese: Like the macaroni, mac and cheese wouldn’t be the same without the cheese. Skip the pre-shredded, which don’t melt as smoothly.
• Gluten-Free Breadcrumbs: To give the casserole a slightly crunchy crust. Don’t go overboard on this ingredient or you’ll lose the gooey cheesy topping.

How to Make Gluten-Free Butternut Squash Mac and Cheese

1. Preheat oven to 400°F.  Spray a 9×13-inch baking dish with non-stick cooking spray.  Place the uncooked butternut squash cubes into the prepared baking dish and bake for 35 to 40 minutes. Once you can easily pierce a fork through the cubes, it is ready. Do not overcook — we don’t want this to brown!
2. Place the cooked butternut squash into the blender and puree. You may have to do this in a few batches depending on the size of your blender. If the squash isn’t blending well, add a tablespoon or two of water to loosen it up. Measure out 1 ½ cups of pureed butternut squash for use in this recipe. The rest can be refrigerated and used for a different recipe or enjoyed as a side dish with another meal.
3. Reduce oven heat to 375°F. Spray another 9×13-inch baking dish with non-stick cooking spray and set aside. You can also clean the one you used to roast the squash. In a large pot that fits at least 2 quarts, cook gluten-free macaroni until al dente. Do not overcook this — we don’t want it to be mushy! Once the macaroni is cooked to al dente, place it in a strainer and rinse with cold water to stop it from cooking further. Also set aside. In an extra-large pot (at least 5 quarts), melt the butter over low heat.
4. Whisk the flour into the butter until it forms a paste. This step needs to be done quickly so that the flour doesn’t start to burn. As soon as a light paste forms (only takes a few seconds), immediately pour the milk and Italian seasoning into the butter mixture. On low-medium heat, bring to a light simmer and continue to simmer and whisk constantly for 5 minutes until the mixture starts to thicken.
5. Remove the pot from the heat and add in 2 cups of the shredded cheddar cheese. Whisk together until the cheese is fully melted.
6. Whisk in the 1 ½ cups of pureed butternut squash until fully mixed. 
7. Pour in the strained macaroni and stir well with a spatula until the macaroni is fully mixed.
8. Use a spatula to place all of the macaroni mixture into the prepared baking dish. Be sure to get all of the sauce out of the pot and into the baking dish. 
9. Sprinkle the remaining 2 cups of shredded cheddar cheese evenly over top of the macaroni mixture.
10. Sprinkle the gluten-free breadcrumbs evenly over top of the shredded cheese. Bake for 25 minutes until the cheese is fully melted. Serve hot.

How to Peel and Roast Butternut Squash

1. Start by cutting off the top and bottom of the butternut squash. 
2. Peel the butternut squash until you get down to the orange flesh. If you still see white/tan skin or streaks of green, you haven’t peeled it enough yet. 
3. Cut the butternut squash in half lengthwise.
4. Scoop out and discard the seeds and stringy flesh.
5. Cut the squash into similar-sized cubes (about 2 inches) so that they cook at the same speed.

Tips for Making the Best Butternut Squash Mac and Cheese

• Shred your own cheese! Pre-shredded cheese contains anti-clumping preservatives that prevent it from melting smoothly.
• Have all of the ingredients and tools you’ll need ready and within reach before you start making this recipe. Once you start making the cheese sauce, you’ll need to whisk constantly to ensure it doesn’t burn.
• Don’t be tempted to add more gluten-free breadcrumbs. If you use too much, they’ll start to soak up the cheesy goodness that makes mac and cheese so delicious.

How Long Does It Take to Make Gluten-Free Butternut Squash Mac and Cheese?

It takes about 40 minutes to roast the butternut squash, 15 minutes to prepare the recipe, then 25 minutes to bake it in the oven. This comes to about 1 hour and 20 minutes of preparation and baking time.

To save yourself some time, you can roast and puree the butternut squash up to 2 days before you need to use it in this recipe.

Storing Gluten-Free Butternut Squash Mac and Cheese

This can be stored in the refrigerator sealed in a food-safe container for 3 to 4 days. To reheat, place the portion you’re going to eat in the microwave for about a minute. The more you reheat the macaroni, the tougher it’s going to become so only reheat a bit at a time and leave the rest in the fridge until you’re ready to enjoy. 

Ingredients Substitutions For Gluten-Free Butternut Squash Mac and Cheese

• Instead of Italian seasoning, you can use ¼ teaspoon of salt, ¼ teaspoon of ground black pepper, plus ½ a teaspoon of garlic powder. Add this in at the same time you add the milk into the recipe.
• Mix up the flavors by adding ¼ cup of shredded Parmesan cheese to the cheddar cheese topping.

Gluten-Free Butternut Squash Mac and Cheese

We’re taking a classic dish and adding in a healthy ingredient! You’ll taste the difference for sure, but the butternut squash doesn’t have an overpowering taste, so even our pickiest eaters at home loved this recipe. It’s a great way to squeeze in some extra vegetables and fall flavor.

More Gluten-Free Pasta Recipes to Try!

• Gluten-Free Mac and Cheese
• Gluten-Free Lasagna
• Gluten-Free Pasta Alfredo
• Gluten-Free Italian Pasta Salad

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