Gluten-free Baked Butternut Squash Mac & Cheese

Gluten-free baked butternut squash mac & cheese, anyone? You know you want some! I am mostly dairy-free, but every once in a while life calls for cheese and this is one of those times! Thanksgiving is coming up so you know I am going to splurge on the dairy! But, the good news is, because of all of the pureed squash, this butternut squash mac and cheese doesn’t require too much cheese – just enough to make it cheesy, but not too much that it’s heavy.

Aside from the butternut squash, my favorite part of this mac and cheese is the sage! Anything with butternut squash is not complete unless there is some sage thrown in there somewhere.

The Roasted Butternut Squash

You will need about a 2-2.5 lb butternut squash, which yields about 4 cups cubed. The roasted butternut squash adds in so much flavor and creaminess to this mac and cheese.

Prepping the Cubed Squash

• Start by cutting the ends from the butternut squash
• Using a vegetable peeler or a sharp knife, carefully peel or trim off the skin from the butternut squash (I prefer using a vegetable peeler). Cut the squash in half lengthwise and scoop out the seeds.
• Place butternut squash cut side down on cutting board and cut into 1/2 inch slices. Cut the slices into about 1/2 inch cubes. Now you’re ready for roasting!

But, let’s be honest about cubing the squash… I don’t know if you guys have noticed but you can buy it already cubed in the grocery store (around fall season). So I’m not going to lie… I sometimes buy it already cubed. However, for this butternut squash mac and cheese, I bought the real thing – to me this recipe is too good to skimp on the experience of getting the entire butternut squash and chopping it up yourself (plus, it’s super easy to do so and not to mention cheaper).

Skipping the Gluten

My absolute favorite gluten-free noodles are by Jovial foods. Their noodles are made with simple, clean ingredients like brown rice and are also organic; it’s not easy to find both. I love penne for this recipe, but any small noodle will work too. And I use almond flour as the crumb topping – turns out great and is so much cleaner than bread crumbs.

If you’re not gluten-free, I recommend whole grain noodles instead and encourage you to try the almond flour topping – it’s that good!

And the Cheese

The key to good mac and cheese is using a combination of cheeses. I use sharp white cheddar (because white cheddar is cleaner as it doesn’t have any additional additives to color it orange) and Parmigiana Reggiano; it’s a perfect match!

And please buy a block and wedge of cheese and shred yourself. For one, it’s cleaner and doesn’t contain added anti-caking ingredients and in addition, freshly shredded cheese melts so much better than pre-shredded.

DISH UP This gluten-free butternut squash mac and cheese is perfect for a main dish or side dish. Serve with a salad, add some chicken, whatever your heart desires.

LOVE PASTA? Check out my skillet vegetable lasagna.

If you make this recipe, please let me know what you think! Leave a comment below and/or share a photo on Instagram and mention @CleanPlateMama!

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5 from 3 votes

Gluten-free Baked Butternut Squash Mac and Cheese

This gluten-free baked butternut squash mac and cheese is light and creamy. The butternut squash gives it a ton of flavor and creaminess and a little bit of cheese keeps it nice and light.

Course Main Course, Side Dish

Cuisine American, Italian

Keyword butternut squash, macaroni, macaroni and cheese

Prep Time 35 minutes

Cook Time 30 minutes

Servings 8 side servings

Calories 619kcal

Ingredients

Ingredients for Macaroni and Cheese

• 2-2 1/2 lb. butternut squash, peeled and cubed about 4 cups cubed
• 1 tbsp. extra-virgin olive oil or avocado oil
• 16 oz penne noodles see notes
• 3 tbsp. butter
• 2 tbsp. gluten-free all purpose flour
• 2 1/2 cups whole milk, divided
• 8 oz sharp white cheddar cheese, shredded see notes
• 4 oz parmigiano reggiano, shredded
• 1 tsp. onion powder
• 1/2 tsp. fine sea salt

Ingredients for Crumb Topping

• 1/2 cup almond flour
• 1 tbsp. extra-virgin olive oil or avocado oil
• 3 tbsp. chopped, fresh sage

Instructions

• Preheat oven to 350.
• Toss cubed butternut squash in 1 tablespoon of oil and spread out on baking sheet. Bake squash for 20-25 minutes, or until you can easily pierce the squash cubes with a fork.
• While the squash is baking, using a large stock pot, cook the pasta according to package and set aside.
• Add the cooked squash and 1/2 cup milk to a high-speed blender. Blend on med/med-high until all squash is pureed. Scrape down sides if needed.
• In a large stock pot (you can use the one you cooked the noodles in) over med-low heat, melt the butter and add the flour; stir until combined. Turn to medium heat and then add in the remaining 2 cups of milk. Stir frequently until the mixture begins to slightly thicken; about 3-4 minutes.
• Add the shredded cheese to the stock pot and mix continuously until all cheese is melted. Add in the pureed butternut squash, onion powder, and salt. Mix until combined.
• Add cooked noodles back to pot with the butternut squash and cheese. Mix until combined and then pour into a 2-2.5 qt. baking dish or 9×11 baking pan.
• In a separate bowl, combine the almond flour, 1 tbsp. oil, and chopped sage. Sprinkle over macaroni.
• Bake uncovered at 350 for 20-25 minutes, or until completely heated through. Sprinkle with additional fresh sage if you have some left over.
• Enjoy!

Notes

• If buying gluten-free, I recommend noodles made from brown rice flour. If using regular noodles, I recommend whole wheat noodles. I like penne for this recipe, but any smaller noodle would work too.
•  Make sure to shred the cheese yourself. Pre-shredded cheese won’t melt as well and won’t turn out the same in this recipe. 
• If you’re limiting your dairy, you can use ghee and almond milk as opposed to butter and cow’s milk. 

Tried this recipe?Mention @CleanPlateMama or tag #cleanplatemama!

Nutrition

Calories: 619kcal | Carbohydrates: 68g | Protein: 25g | Fat: 28g | Saturated Fat: 14g | Cholesterol: 59mg | Sodium: 605mg | Potassium: 783mg | Fiber: 6g | Sugar: 9g | Vitamin A: 15725IU | Vitamin C: 30mg | Calcium: 574mg | Iron: 3mg

Please note all nutrition information is based on third-party calculations. These are estimates and exact values may vary based on portion, measuring accuracy, and brands used.