Butternut Squash Mac n’ Cheese

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Three cheeses. Roasted butternut squash. Pasta. Sounds pretty perfect, right? This butternut squash macaroni and cheese is the fall recipe your family needs. Everyone will love it, and it makes amazing leftovers. So what are you waiting for? Head to the store and grab your ingredients!

Baked macaroni and cheese in a clear baking dish with a wooden spoon, on a wooden table, a blue table cloth, with rosemary, cheese, and a butternut squash in the background.

why you should make this recipe

First, this butternut squash macaroni and cheese is delicious. Like, beyond delicious. But the real reason to make it? It’s an easy macaroni and cheese recipe that the whole family will love. Hear me out: this recipe is backed with veggies (and therefore, less cheese than a typical macaroni and cheese), but these hidden veggies will trick even the pickiest of eaters. So, this. butternut squash macaroni and cheese is delicious, mom-approved, and kid-friendly. Perfect.

Ingredients: olive oil, milk, onion, butternut squash, cheeses, garlic, pasta, rosemary

ingredient notes

  • Nutmeg – Just a pinch, but it adds to the fall flavor of this macaroni and cheese recipe.
  • Parmesan Cheese – My favorite way to top off baked mac! Add on top before baking (like you would breadcrumbs). Extra cheese = extra yum!
  • Butternut Squash- You can buy this pre-cubed, or peel and cube it yourself! The butternut squash is subtly sweet and gets soooo creamy when you purée it!

how to make this recipe your own

  • Add (more) veggies- Sometimes, I’ll add a bunch of roasted vegetables to this dish (like roasted brussels), to beef it up but still keep it vegetarian-friendly!

recipe faq’s

How long can I keep this in the fridge?

I’d say that this butternut squash macaroni and cheese will stay good for about 4-5 days after making it, as long as you keep it in an airtight container in the fridge!

Enjoy, and as always, please let me know if you make this recipe – and if you do, don’t forget to tag @seasonedandsalted and #seasonedandsalted on Instagram!

Baked macaroni and cheese in a clear baking dish with a wooden spoon, on a wooden table, a blue table cloth, with rosemary, cheese, and a butternut squash in the background.

Butternut Squash Mac n’ Cheese

Allie Hagerty
This butternut squash macaroni and cheese recipe is creamy, cheesy, and oh so delicious. It's kid-friendly and parent-approved, too!
5 from 1 vote
Prep Time 15 minutes
Cook Time 45 minutes
Total Time 1 hour
Course Main Course, Pasta
Cuisine American
Servings 8 servings
Calories 511 kcal


  • measuring spoons
  • measuring cups
  • cutting board
  • chef’s knife
  • mixing bowls
  • sheet pan
  • whisk
  • parchment paper
  • non-stick pan
  • baking dish
  • food processor


  • 20 ounces cubed butternut squash peeled and de-seeded
  • 1 white onion
  • 2 cloves of garlic
  • 1 tablespoon olive oil
  • Kosher salt and pepper
  • 1 pound pasta I love shellbows, but you can use macaroni or cavatappi
  • 2 1/2 cups 1% milk
  • 2 tablespoons unsalted butter
  • 3 tablespoons flour
  • 1/8 teaspoon ground nutmeg
  • 2 tablespoons chopped fresh rosemary
  • 1 tablespoon fresh rosemary
  • 1 cup white cheddar cheese shredded
  • 1 cup sharp orange cheddar cheese shredded
  • 1/4 cup grated parmesan cheese
  • 1/4 cup breadcrumbs
  • 1 1/2 teaspoons salt
  • 1 teaspoon freshly cracked black pepper


  • Preheat your oven to 400°F. Spread the cubed butternut squash, sliced onion, and crushed garlic cloves on a baking sheet lined with parchment paper. Drizzle olive oil over the the veggies and toss before sprinkling with a pinch of salt, pepper, and nutmeg. Roast the veggies for 25 minutes. Grease a 9 x 13 baking dish (or whatever you have on hand), and set it aside for later.
  • While the vegetables are roasting, cook your pasta according to the package. Once it’s done, strain the pasta and set it aside in a large bowl.
  • Next, it’s time to make your butternut squash purée! Add the butternut squash, onions, and garlic to food processor and purée until smooth. Next, add ½ cup milk and purée a little bit longer. The purée should smoothen out a bit with the addition of the milk. Leave the puree in the bowl it’s in – we will need it again in a few minutes.
  • Now, let’s make the roux and the base of the butternut squash sauce. Grab a large nonstick pan and place on your stove. Heat butter in the pan over medium heat until it has melted. Next, add the flour. Using a whisk, mix the flour and butter together until it starts to smell nutty and fragrant — it will be a bit clumpy, and thats okay. Do this for 2-3 minutes or so.
  • Add the remaining milk (2 cups) to then pan and whisk until the liquid has combined with the flour mixture, and eventually smooths out. Once smooth, turn up the heat and bring the mix to a boil (continue to whisk during this time). The sauce will gradually thicken. Once it thickens, turn your heat back down to low before adding the fresh rosemary, thyme, and then butternut squash purée.
  • Mix the ingredients together until they are well-combined, before taking the pan off the heat. Pour the sauce over the cooked pasta from before that is now (hopefully) in a large bowl.
  • Pour half of the sauced pasta into the prepared baking dish. Then layer half of the cheddar cheeses. Repeat the process with the remaining pasta and cheddar cheeses. Then, sprinkle 1/4 cup breadcrumbs and 1/4 cup grated parmesan cheese on top.
  • Bake for 25-30 minutes (uncovered), until bubbling and hot. Remove from the oven and let rest for 5-10 minutes.


Make sure to cook your noodles al dente! 


Calories: 511kcalCarbohydrates: 56.6gProtein: 22.7gFat: 20.9gSaturated Fat: 11.5gPolyunsaturated Fat: 0.3gMonounsaturated Fat: 2.3gCholesterol: 57.5mgSodium: 838.9mgPotassium: 167.2mgFiber: 3.9gSugar: 5.7g
Keyword butternut squash, Fall, mac n cheese
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