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.Jump to Recipe
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 gluten-free baked mac and cheese is the sage! Anything with butternut squash is not complete unless there is some sage thrown in there somewhere.
Roasting 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 gluten-free baked 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). After the squash has been peeled, 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 cubed squash is 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).
How to Make Baked Butternut Squash Mac and Cheese
- Roast the cubed butternut squash in oven (see section above for specifics on cutting the squash).
- While the squash is roasting, cook pasta according to package directions and set aside. Tip: do not overcook pasta as it will continue to cook once you transfer to the oven for baking.
- Puree the cooked squash and milk in a high-speed blender.
- In a large stock pot, melt shredded cheeses into the remaining milk over medium heat.
- Add the pureed butternut squash, onion powder, and salt to the cheese/milk mixture. Stir until combined.
- Add cooked noodles to pot with butternut squash and cheese mix and mix well. Pour mac and cheese into a baking dish.
- In a separate bowl, prepare the crumb topping by combining the almond flour, extra-virgin olive oil, and sage. Sprinkle over macaroni and cheese.
- Bake at 350 for 20-25 minutes, or until edges are set and mac and cheese is heated through. Sprinkle with additional fresh sage.
- Serve and enjoy!
How To Keep This Gluten Free
First off, you will need to use gluten-free noodles to keep this butternut squash mac and cheese gluten free. My absolute favorite are Jovial gluten-free Penne noodles. Their noodles are made with simple, clean ingredients and they are organic; it’s not easy to find both.
Lots of mac and cheese recipes call for a roux (butter/oil and flour mixed together), which is used to help thicken the cheese sauce. The butternut squash in this recipe helps to thicken the cheese sauce, so I skip the roux all together.
In addition, I use almond flour as the crumb topping – turns out great and is so much cleaner than bread crumbs (which is what is typically used for crumb topping).
NOODLES – This recipe calls for gluten-free penne noodles. But any tube shaped noodle will work. If you aren’t gluten-free, or prefer a different noodle, any noodle should work. If using wheat noodles I recommend whole wheat to keep them whole grain (considered a real food).
CHEESE – a combination of cheeses is key to this butternut squash baked mac and cheese recipe. I use sharp white cheddar and Parmigiana Reggiano. I would for sure use cheddar. You could use all cheddar, or switch it up and try Gruyer or Swiss instead of the Parmigiana Reggiano.
CRUMB TOPPING – most baked mac and cheese in the oven calls for Panko bread crumbs for the topping. To keep this gluten free, I use almond flour. The texture of almond flour resembles bread crumbs, plus I really like the nutty flavor it adds to the final dish. If you don’t like/want almond flour, you could look for gluten-free Panko (although not clean), or skip all together. Or instead of a crumb topping, you could just add some extra shredded cheese on top to get a nice, crisp layer of cheese.
Tips For Keeping The Ingredients Clean
NOODLES – as I mentioned earlier, look for brown rice noodles (this keeps it whole grain). If you aren’t gluten free, look for whole wheat noodles (look at the ingredients to ensure only whole wheat, or whole durum wheat flour is listed). With grains, I prefer organic as well to limit the expose to chemicals that are sprayed on the grains.
CHEESE – make sure to buy blocked cheese. Pre-shredded cheese has an anti-caking ingredient added, so it takes away from it being clean. Plus, block cheese that is freshly shredded melts MUCH better. Also, buy white cheddar so you don’t have the additional ingredients added to color it orange. With all things dairy, organic is best (if it’s an option for you) to stay away from hormones, antibiotics, and GMO feed.
MILK – look for organic. Same as cheese, organic is best (if it’s an option for you) so you aren’t getting antibiotics and hormones in your milk.
BUTTERNUT SQUASH – because the squash has a thick outer skin that you throw away, you don’t need to worry about whether organic is better/cleaner. Go ahead and buy conventional without any worry.
Other Side Dishes I Think You’ll Love
If you make this gluten free baked butternut squash mac and cheese, please let me know what you think! Leave a comment below and/or share a photo on Instagram and mention @CleanPlateMama!
Gluten-free Baked Butternut Squash Mac and Cheese
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 gluten-free penne noodles (see notes)
- 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
- 1/4 cup chopped, fresh sage
- Preheat oven to 350.
- Toss cubed butternut squash in 1 tablespoon of oil and spread out squash on a 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) add in the remaining 2 cups of milk and shredded cheeses. Stir 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 glass baking pan.
- In a separate bowl, combine the almond flour, 1 tbsp. oil extra-virgin olive 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.
- Make sure to buy block cheese and shred the cheese yourself. Pre-shredded cheese won’t melt as well and won’t turn out the same in this recipe.
- Don’t overcook the noodles. They will continue to cook when you bake the mac and cheese. They can even be slightly underdone after you boil them (but not crunchy still).
- I prefer Penne noodles, but any tube shaped noodle will work. If not gluten-free, look for whole wheat noodles (it’s a whole grain, so keeps it a real food).