Dinner Recipes/ Recipes/ Sides and Sauces

Gluten Free Butternut Squash Macaroni and Cheese

Gluten Free Butternut Squash Macaroni and Cheese has all the deep, creamy flavor of macaroni and cheese with hidden veggies!

Gluten Free Butternut Squash Macaroni and Cheese scooped from panProduct for this post was provided by Full Flavor Foods. No monetary compensation was given, all opinions are my own.

Macaroni and Cheese

Macaroni and Cheese has always been one of my favorite foods. My Granny always made the best mac & cheese. I couldn’t wait to visit to visit and eat a huge helping.

My daughter has the same love. She asks for “Moni Moni” on an everyday basis. She know how to say macaroni, but loves calling it moni moni, no idea why!

The other day we were on our biweekly Mother/Daughter Trader Joe’s trip and saw that they had Butternut Squash Macaroni and Cheese. I hoped it was gluten free, but it wasn’t, so I decided to make my own!

Pan of gluten free butternut squash macaroni and cheeseGluten Free Butternut Squash Macaroni and Cheese

I was so excited to give it a try. It seemed pretty simple- just add some butternut squash to a cheesy sauce and it would be perfect. It took a little more trial and error than I thought, but eventually, I figured out the perfect ratio for this cheesy goodness.

My husband ate half the pan. I couldn’t believe it. Then his friend came over and finished it off. It was so creamy with tons of flavor. The secret is 3 kinds of cheese and my Full Flavor Foods cream sauce mix.Gluten Free Macaroni and Cheese Plate with Full Flavor Foods Cream Sauce Mix

You can totally make a traditional roux with gluten free flour, but the cream sauce mix already has all the seasonings and is as simple as adding water. I have a big bag and use it for everything from quick soups, sauce for salmon and chicken, and dishes like this Gluten Free Butternut Squash Macaroni and Cheese.

Gluten Free Butternut Squash Macaroni and Cheese up close bite

Recipe Notes

This creamy Gluten Free Butternut Squash Macaroni and Cheese is really easy to make. Just a few notes to help make it go smoothly.

Gluten Free Pasta-

I used a 12 ounce box of pasta. I used Ronzoni for this because there was an Ibotta coupon and I got it for $1.00. Barilla for baked pasta, but honestly, you can use whatever pasta is your favorite. We eat the Trader Joe’s Brown Rice and Quinoa a lot. Just be sure to cook it al dente or it will get mushy. If it doesn’t give you an al dente time, just reduce the cook time by 2 minutes.


Cheese makes macaroni and cheese good. Now is not the time to skimp or use reduced fat versions. I used a cup of gouda, a cup of sharp cheddar and half a cup of parmesan. It sounds like a lot, but there is squash in this, so I figure it evens itself out! If you need a vegan mac & cheese, try this Creamy Vegan Mac & Cheese from Veggie Balance.

Bread Crumbs-

This time around I used Schar, but use whatever you can find. You can even make your own if you have a couple slices of stale gluten free bread. If you don’t have any, this recipe can be made without them.

Butternut Squash-

I used some precut up squash that I roasted, but half a whole butternut squash is what you need. You will want a total of 1 cup butternut squash puree.

Cream Sauce-

Full Flavor Foods Cream Sauce is perfect for this. It is available in stores up north and in a few smaller stores down south, it can also be purchased online in large bags, which is amazing. If you can’t find it, you can make a traditional roux with gluten free flour and seasoned with salt and pepper, you will need 1 and a 1/2 cups.

You can learn more about Full Flavor Foods by checking out my Gluten Free Chicken Pot Pie Muffins. I’ve been so impressed with their products. I’m about done using all my samples and will be purchasing more soon!

I’m totally in love with Butternut Squash this season- if you are looking for another way to combine Butternut Squash and pasta check out Mi Gluten Free Gal’s Butternut Squash Lasagna for Two. It’s next on my list to make!

Need even more veggie side dishes? These Roasted Brussels and Carrots from Vegetarian Mama look divine! If you are looking for a vegan version of mac and cheese, try this Best Vegan Mac and Cheese from Allergylicious! More comfort food recipes? Try this Quick Beef Stew from Healthy Seasonal Recipes!

For those of you who prefer to substitute pasta for a veggie, this Sausage Spaghetti Squash from Sun Kissed Kitchen or 6 Ingredient Butternut Squash Noodles from Foolproof Living would be great!

Love  a great casserole- try this Buffalo Chicken Casserole from The Clean Eating Couple and add this Massaged Kale Salad from Healthy Seasonal Recipes to go with!

What’s your favorite Macaroni and Cheese memory? Let us know in the comments!

Happy Gluten Free Eating!

Gluten Free Butternut Squash Macaroni and Cheese on a plate
Print Recipe
5 from 2 votes

Gluten Free Butternut Squash Macaroni and Cheese

Gluten Free Butternut Squash Macaroni and Cheese is the perfect comfort food for fall. Full of creamy cheeses and butternut squash, everyone will be back for seconds.
Prep Time15 minutes
Cook Time15 minutes
Total Time30 minutes
Servings: 12 servings


  • 12 ounce box of gluten free pasta cooked al dente
  • Full Flavor Foods Cream Sauce and 1 1/2 cups water or 1 1/2 cups traditional roux made with gluten free flour
  • 1 cup butternut squash puree
  • 1 cup shredded gouda
  • 1 cup shredded sharp cheddar
  • 1/2 cup parmesan
  • 1/4 cup bread crumbs
  • 1/4 teaspoon salt
  • pinch of pepper
  • 1/4 teaspoon garlic powder
  • 1 Tablespoon dried parsley
  • 1/2 Tablespoon melted butter


  • Pre-heat oven to 350 degrees.
  • Boil pasta to al dente, according to package directions.
  • Make cream sauce according to package directions.
  • Whisk in butternut squash, 3/4 cup gouda, 3/4 cup cheddar, and parmesan.
  • Add in pasta and mix together carefully.
  • Pour into pan.
  • Sprinkle with remaining cheese.
  • Combine bread crumbs, salt, pepper, garlic powder and parsley.
  • Sprinkle bread crumbs over macaroni and cheese.
  • Lightly spray a sheet of aluminum foil with cooking spray.
  • Cover macaroni and cheese with foil and bake for 10 minutes at 350 degrees.
  • Remove foil and cook for 5 minutes longer.
  • Serve.

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  • Reply
    Gluten-Free Butternut Squash Lasagna for Two - MI Gluten Free Gal
    January 1, 2019 at 2:32 pm

    […] for something a little more “traditional”? Try Eat At Our Table’s Gluten-Free Butternut Squash Macaroni and Cheese. Your kids wont’ know they’re eating […]

  • Reply
    Sharon @ What The Fork
    October 28, 2017 at 11:52 am

    This looks like such a great mac and cheese!

  • Reply
    Karyl | Karyl's Kulinary Krusade
    October 25, 2017 at 4:34 pm

    I am obsessed with macaroni & cheese! I’ve never thought to add butternut squash…great way to extend the recipe, and add a healthier kick

  • Reply
    Gluten Free With Emily
    October 25, 2017 at 3:26 pm

    I love making Squash Mac N Cheese. So nourishing this time of year!

  • Reply
    October 25, 2017 at 3:11 pm

    That looks delicious! I l Be butternut squash and I think it’s a perfect combo you have here.

    • Reply
      October 25, 2017 at 3:12 pm

      I meant I love butternut squash. Sorry for the typo error.

  • Reply
    Nicole Dawson
    October 25, 2017 at 1:36 pm

    Looks so creamy & delicious Amanda. Definitely a healthier twist on a much loved comfort food.

  • Reply
    Sami Summers
    October 25, 2017 at 1:32 pm

    I am in love with this recipe! Definitely going to have to try it out soon. Anyway that I can sneak more veggies into Hubs’ diet is good in my book.

  • Reply
    Alisa Fleming
    October 25, 2017 at 11:48 am

    Butternut squash adds such amazing consistency and color to sauces – I love the way you used it here Amanda!

  • Reply
    October 25, 2017 at 12:21 am

    that topping on that looks AMAZING!!! and gouda??? YES PLEASE.

  • Reply
    October 24, 2017 at 8:07 pm

    we love mac & cheese too, and I love to sneak additional nutrients in like this… yours looks SO good!

  • Reply
    Paula @ I'm Busy Being Awesome
    October 24, 2017 at 7:06 pm

    Macaroni and Cheese was my FAVORITE FAVORITE food when I was younger…and not the fancy stuff, the kind from the box ? In fact, my uncle got me something like 20+boxes for Christmas one year, and only as a semi-joke. Ha!

  • Reply
    October 24, 2017 at 5:33 pm

    I love the addition of squash in here. Perfect for a wonderful fall meal!

  • Reply
    Chrystal @ Gluten-Free Palate
    October 24, 2017 at 2:36 pm

    Oh my gosh. I so, so want this for lunch today!

  • Reply
    October 24, 2017 at 10:07 am

    In my house, I couldn’t call this butternut squash mac & cheese. I’d have to just call it mac & cheese. 😉 But I love scamming veggies on my family and this is one way I didn’t think of. Pinning!

    • Reply
      October 24, 2017 at 2:21 pm

      I understand that! The butternut squash blends in so well, it’s an easy way to sneak in veggies!

  • Reply
    Emily - The Southern Belle Blogs
    October 24, 2017 at 8:46 am

    Oh yum! That looks amazing! I love using butternut squash in usual ways and mac and cheese is such the perfect comfort food.

    • Reply
      October 24, 2017 at 2:22 pm

      I love creative ways to use butternut squash as well!

    5 from 2 votes (2 ratings without comment)

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