Today, we’re going to revisit a recipe that was originally posted on the blog back in 2014. Over the years, this recipe has become a family favorite as well as a favorite with many reader friends and their families. This recipe is a fall twist on classic, homemade, and, yes, healthy macaroni and cheese.

This macaroni and cheese is made with nourishing, real ingredients; not the ultra-processed ingredients you’ll find in most (pretty much all) store-bought mac and cheese boxes.

Butternut Squash Macaroni and Cheese Recipe Gluten Free

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Real food is about eating seasonally. Broccoli and peaches aren’t grown year-round, instead there’s a specific season in which broccoli and peaches are grown. This is true for all real food, including real dairy and even meat. This is a beautiful thing, because it means that we were intended to eat variety and in a very sustainable way! Our body needs a variety of nutrients, and a seasonal shift in food provides us with this variety in a very natural and delicious way. (Learn all about real food here.)

roasted butternut squash

It’s important to get comfortable in the kitchen and learn how to prepare seasonal foods instead of always reaching for the out-of-season broccoli. The good news is you don’t need a ton of unique recipes (or a million Pinterest boards) to learn how to prepare a variety of seasonal ingredients. Instead, you simply need to learn a few techniques that you can use to prepare a variety of foods. These techniques include pickling, fermentation, roasting, and making amazing salads.

Roasted Butternut Squash

Roasting is definitely one of the easiest and most versatile techniques to learn. If you find a veggie at the market or store and you have no idea what to do with it, roasting is usually a sure way to prepare it.

Roasting brings out the natural sweetness in veggies, which makes them a kid favorite. Even if your kids don’t love steamed veggies, I bet they’ll go for the roasted version of that veggie.

Today’s recipe calls for roasting a butternut squash to make a fall version of macaroni and cheese. So let’s talk about how to roast a butternut squash.

roasted butternut squash

How to Roast a Butternut Squash

There are a couple of options for roasting a butternut squash. The method you choose depends on whether you purchase a whole butternut squash or pre-cut cubes.

The first option, a whole butternut squash, requires more effort to prepare. This is the most common way to purchase butternut squash. The second option, pre-cut cubes, can be found in the produce department at many stores. I know Whole Foods (where I do a lot of my shopping) always has peeled and cut butternut squash available.

Roasted Butternut Squash (Whole)

If you go with a whole butternut squash, the easiest and most effortless way to roast it is to cut the squash in half using a sharpened chef knife. Once split open, remove the seeds with a spoon. Then rub the skin with extra virgin olive oil or avocado oil, sprinkle with salt, and flip the squash over on a sheet pan or baking dish so the flesh faces down.

Roast the whole squash, covered with foil, at 425F for about 45 minutes to an hour, depending on thickness and size. The squash is ready when the skin begins to shrivel and feels soft to the touch. Once the whole squash is cool to touch, scoop the flesh away from the skin. The skin may be composted or discarded and the flesh may be enjoyed mashed, blended in a soup, blended with mashed potatoes, or in this macaroni and cheese recipe.

roasted butternut squash (cubes)

The easiest way to go about roasting pre-cut cubed butternut squash is to place the cubes in a baking dish or a sheet pan and drizzle the squash with olive oil (or you could add a few cubes of butter instead of oil) and sprinkle with salt. Roast the squash at 425F for about 25-30 minutes, depending on the size of the cubes. The squash is ready once soft. Once ready, enjoy the squash as a side, blended in a soup, or use the squash to make today’s macaroni and cheese recipe.

How to Make Butternut Squash Macaroni and Cheese

Once you’ve roasted a butternut squash, you can use the flesh in a variety of ways. I’ll share a few more ideas in a few minutes. First, let’s talk about how to use the roasted butternut squash to make macaroni and cheese.

Cooking pasta

While the squash cooks in the oven, cook macaroni pasta on the stove-top. My preference is Jovial’s brown rice pasta. If you use brown rice pasta, or a bean pasta (which I have yet to try), the macaroni and cheese will be safe for anyone with a gluten allergy.

blending butternut squash to make the cheese sauce

After roasting the butternut squash, place the squash in a blender or food processor along with juices from the pan and puree the squash until smooth. Alternatively, you could mash up the squash in a bowl until it reaches a pureed consistency.

adding butternut squash to the pot to make cheese sauce

From there, melt butter in a soup pot or Dutch oven (reuse the pot used to cook the pasta), add milk, mustard powder (optional), salt, and the butternut squash puree. Allow this mixture to thicken and then add cheddar and parmesan cheese. Return the noodles to the pot and mix the sauce with the noodles. Bake the macaroni and cheese and serve!

Adding milk to the pot to make the cheese sauce

This recipe makes plenty for a family (serves 6-8 people), so lunch leftovers are usually a guarantee. I recommend reheating the macaroni and cheese in a skillet with a bit of milk (or the microwave) and serving in a thermos if you’re going to pack the leftovers for lunch. (See my favorite lunch gear here.)

shredding cheese for mac and cheese

How to Serve Butternut Squash Macaroni and Cheese 

Serve butternut squash macaroni and cheese as a main dish alongside a salad (learn how to make an AMAZING salad) and homemade vinaigrette. Or, serve this macaroni and cheese on the side of roasted chicken (the chicken can roast while the butternut squash cooks) or protein of choice.

macaroni and cheese being stirred in a pot

How to Prep This Recipe in Advance

As you know, I’m all about prepping in advance in order to simplify real food. If you want to make this macaroni and cheese during the week and don’t have much time to spend in the kitchen, here are a few ways to do this…

Cook and puree the squash in advance. Store the pureed squash in an air-tight container (here are my favorite storage containers) in the fridge for up to 4 days. You can add the cold squash directly to the milk and butter when you’re ready to make this dish.

Prep the entire dish in advance (roast the squash, make the cheese sauce, cook the pasta), but don’t bake it. Store the mac and cheese in the fridge (covered) for up to 1-2 days. Bake the macaroni and cheese when you’re ready.

Make the macaroni and cheese and freeze the meal for the future. To do this, follow the instructions in the recipe but don’t bake the dish. Once the macaroni and cheese is added to a freezer and oven-safe baking dish, freeze the tightly wrapped macaroni and cheese. To cook, preheat the oven to 425F. Remove the macaroni and cheese from the freezer, uncover, allowing the macaroni and cheese to defrost while the oven preheats. Bake for 30 minutes, until bubbly.

Butternut squash mac and cheese ready for the oven

More Ways to Use Butternut Squash 

Now that fall is officially here and we know the importance of adding a variety of seasonal foods to our diet, like butternut squash, here are a few more ways to use butternut squash beyond this macaroni and cheese recipe. You may notice that every recipe calls for roasting the squash first. This is why learning to roast veggies is so important. Once you learn this basic cooking technique, you can use the roasted veggie to make a variety of delicious meals.

Butternut Squash Mac and Cheese in a bowl
Butternut Squash Macaroni and Cheese Recipe Gluten Free
Butternut Squash Macaroni and Cheese Recipe Gluten Free
4.72 from 7 votes

Roasted Butternut Squash Macaroni and Cheese

Butternut squash is amazing when roasted, so this recipe calls for roasting the squash, then pureeing and creating an extra creamy butternut cheese sauce and then baking the macaroni and cheese for a final show-stopper. Gluten-free and freezer-friendly.
Kristin Marr
Prep Time25 minutes
Cook Time1 hour 10 minutes
Total Time1 hour
Course Main Course, Side Dish
Cuisine American
Servings 8 People
Calories 471 kcal


  • 3 lb butternut squash whole or pre-cut cubes (see instructions for how to roast either option)
  • 1 TB extra virgin olive oil or avocado oil or 2 TB cubed unsalted butter (for roasting the squash, see the instructions for details)
  • 3 garlic cloves
  • 4 TB unsalted butter
  • 12 ounces macaroni noodles 12-16 ounces of pasta, this will depend on the brand you use, both options work.
  • 2 cups whole milk
  • 1 tsp ground mustard (optional)
  • 1 tsp salt to taste, plus extra for roasting
  • 2 cups shredded cheddar cheese
  • 1/4 cup grated parmesan cheese (optional)

Special Equipment


Roast the Butternut Squash and Cook the Pasta:

  • Preheat the oven to 425F.
  • If you're using a whole butternut squash: Line a sheet pan or baking dish with parchment paper for easy cleanup (optional). Cut the squash in half using a sharpened chef knife. Once split open, remove the seeds with a spoon. Then rub the skin with 1 tablespoon of extra virgin olive oil or avocado oil (divided amongst each half), sprinkle with salt, add the garlic cloves to the cavity of the squash (either just one or both) and flip the squash over on a sheet pan or baking dish so the flesh faces down. Cover the pan with foil and roast for 30 minutes, then remove the foil and continue to roast the squash until soft (about 15-30 more minutes, depending on the size of your squash). 
  • If you're using pre-cut cubed butternut squash: Line a baking dish with parchment paper for easy cleanup (optional). Place the cubes in the baking dish and drizzle with olive oil to lightly coat the squash (or you could add 2 tablespoons of unsalted butter throughout the squash cubes instead of using oil), add the garlic cloves, and sprinkle with salt. Roast the squash, uncovered, at 425F for about 25-30 minutes, depending on the size of the cubes. The squash is ready once soft.
  • While the squash roasts, cook the macaroni noodles according the package on the stove-top. Once cooked, drain the pasta and set aside.

Make the Macaroni and Cheese:

  • Reduce the oven temperature to 375F.
  • Place the roasted squash, garlic cloves and “juice” leftover from roasting the squash in a blender or food processor, puree for 20 seconds until smooth. If you roasted a whole squash, you'll need to scoop the flesh away from the skin and place the flesh in the blender. If you roasted cubed squash, add all the ingredients directly to the blender. If there aren't enough juices to puree the squash, add a bit of olive oil or water to help get things moving.
  • Heat 4 tablespoons of butter in a large soup pot or Dutch oven (reuse the pot used to cook the pasta). Add the milk, mustard powder (if using), salt, and butternut squash puree. Whisk the ingredients until smooth and combined. Cook on medium-low heat until slightly thickened, around 5 minutes.
  • Once thickened, add the cheddar cheese and (if using) 1/4 cup of parmesan cheese.
  • Whisk the cheese into the sauce. Simmer the mixture, stirring frequently, until thickened (just a few minutes). Add the macaroni noodles to the cheese sauce and stir to combine.
  • Place the cooked macaroni and cheese in a 13×9 baking dish. Top with additional parmesan cheese (optional).
  • Cook, uncovered, for 20-25 minutes until the cheese bubbles and the cheese sauce thickens.


Gluten-Free Notes: This sauce contains no flour so this recipe is naturally gluten-free. Use brown rice pasta (I love Jovial brand) or a bean pasta. 


Calories: 471kcalCarbohydrates: 57gProtein: 19gFat: 19gSaturated Fat: 11gCholesterol: 54mgSodium: 548mgPotassium: 569mgFiber: 4gSugar: 7gVitamin A: 10552IUVitamin C: 20mgCalcium: 368mgIron: 2mg
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  1. Hi, I prepared this before my newborn arrived and froze it in the 9×13 pan. Do you recommend baking from frozen or thawing first? I had found this via a freezer meal search but realize now that I don’t see instructions from frozen. Thanks!

    1. Many mac and cheese recipes require baking after cooking the noodles. You could skip the baking if desired and try experimenting with just a stove-top version.

  2. I haven’t yet made this and am curious if cooking the pasta ahead of time, then baking it in the sauce for 20-25 minutes, doesn’t over-soften the noodles. I’m guessing it’s not a problem as no one has commented on this but I don’t like mushy pasta so I wanted to ask. Could the pasta be baked uncooked or would more moisture be required?

    1. Hi Lydia,

      Many mac and cheese recipes require baking after cooking the noodles. You could skip the baking if desired and try experimenting with just a stove-top version.

      LS Team

      1. Hi,

        My question was about skipping the cooking part, not the baking. I would rather pour the mixture over raw noodles to have one less prep step. I think I will try cooking them raw next time because by following the recipe, the noodles indeed turned out too soft for my liking.

      2. I’m sorry about that Lydia. Yes, you can definitely try that. I hope they turn out better for you!

        LS Team

  3. Just made this delicious recipe. Next time, I’ll reduce the amount of garlic as it felt a touch overpowering.

  4. 5 stars
    I cannot thank you enough for this recipe. I’m currently in the nesting period during my first pregnancy and trying new recipes that will be freezer friendly and help make the transition period after baby comes more easy. I stumbled across this recipe on Pinterest and immediately added it to the “try” list. For Sunday dinner, I made this to accompany a pot roast for my full family. Everyone loved it. Even my brother who has always been a picky eater had second and third helpings. To find a healthy and delicious comfort food such as this is so important to our family at any time, but especially now that it’s growing. Thank you so much. And thank you for this blog which has helped me to approach meal planning and real food eating prep without feeling so overwhelmed. Your time and effort are so greatly appreciated.

  5. 5 stars
    Oh, it looks so delicious! Are there people who don’t like macaroni and cheese? As for the ability to cook seasonal vegetables, you are absolutely right. As a rule, we generally forget about them during the season, or prepare 1-2 dishes and they start to annoy us. Most likely, this is because we do not bother with the preparation of really diverse and new dishes. I really liked your blog, now I will come here again quite often, thanks for the creative ideas and non-primitive recipes!

  6. Kristin, could you recommend an alternative (perhaps dairy-free) to whole milk? I would like to eliminate the lactose (I guess I could consider a lactose-free 2%) and also reduce the fat a bit since the recipe also calls for 6 tbsp butter & the cheese. My guess is that anything other than whole milk would affect the creamy texture, but hoping you might have a good suggestion. Thank you!

    1. Hey Catherine, You could do coconut cream or coconut milk, or almond milk. (Real) fat (in the form of grass-fed butter and real cheese) is so good for you, and really makes this delicious, so I would keep it ;).

    1. Hey Stephanie, I have an IP mac and cheese recipe coming up soon. Hmmm, I think you might be able to use butternut squash puree in the recipe, but I’m not sure how you’d cook the noodles and squash in the Instant Pot at the same time. Well, that is unless I tested it ;). I can email you the recipe if you’d like to play around with adding butternut squash puree.

  7. 5 stars
    Just cooked this recipe tonight for supper! So yummy! I did not have milk so i substituted sour cream i had plus some homemade chicken stock. So creamy! Family loved it! I see why you would use sharp cheddar to compensate for the sweetness of the squash maybe? Will be making this again:)

  8. Something must be going right with this dish if the first two people to post comments are named Grace! As far as I know, we are no relation.

    Anyway, this recipe looks fabulous. In fact, I like it so much that I featured it today as the Recipe of the Day on my Facebook page, Cooking with Whole Grains & Real, Whole Foods, and I’ve added butternut squash to my shopping list today.

    I’m so sorry you and your youngun’ got sick on your dreamy vacation and missed out on a lot of the fun. Hope you get to enjoy it more next time.

  9. Hi,just made this recipe, but reduced it by half to make in an 8×8 size baking pan. I steamed the butternut cubes, which I purchased pre-cut.
    As blending the cooked butternut squash, I added, garlic salt, and garlic butter.
    I chose your recipe to sneak in vegetables to the main meal; next I need to find more entree recipes with fruit baked.

  10. Do you think this would do ok if cooked and then frozen? It made way more than we needed for one meal and leftovers will not eaten right away…

  11. About how much squash do you think this is in cups? I just diced up a whole bunch and needed 8 cups -ish for a squash soup and I have about that much left (diced). I think the 8 cups is approx. three pounds. This sounds great!