Butternut Squash Macaroni and Cheese Recipe Gluten Free
5 from 4 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.

Course Main Course, Side Dish
Cuisine American
Keyword Butternut Squash Macaroni and Cheese
Prep Time 25 minutes
Cook Time 1 hour 10 minutes
Total Time 1 hour
Servings 8 People
Calories 471 kcal
Author Kristin Marr


  • 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:

  1. Preheat the oven to 425F.

  2. 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). 

  3. 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.

  4. 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:

  1. Reduce the oven temperature to 375F.

  2. 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.

  3. 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.

  4. Once thickened, add the cheddar cheese and (if using) 1/4 cup of parmesan cheese.

  5. 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.

  6. Place the cooked macaroni and cheese in a 13x9 baking dish. Top with additional parmesan cheese (optional).

  7. Cook, uncovered, for 20-25 minutes until the cheese bubbles and the cheese sauce thickens.

Recipe Notes

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.