Butternut Squash Mac and Cheese

Creamy, cheesy, and SO delicious, this butternut squash mac and cheese is the ultimate fall comfort food. It'll be a hit with the whole family!

Butternut squash mac and cheese

Butternut squash mac and cheese! If you thought the Trader Joe’s version was good, you’ll LOVE this homemade one.

I adapted the recipe from my traditional macaroni and cheese. Instead of making a roux with flour and butter, I used pureed roasted squash as the base of the cheese sauce. The squash makes it insanely creamy (even creamier than classic mac!) and adds a subtle sweetness to the rich, cheesy flavor. Bonus: it sneaks in some extra nutrients too!

This butternut squash mac and cheese has been a huge hit in our house. It’s comforting, delicious, and—thanks to the squash—just perfect for fall. I can’t wait for you to try it!

Butternut mac and cheese recipe ingredients

Butternut Squash Mac and Cheese Ingredients

Here’s what you’ll need to make this butternut squash mac and cheese recipe:

  • Butternut squash, of course! Look for one on the larger side. You’ll need 2 cups of soft roasted squash to make the creamy sauce.
  • Pasta – Shells are my shape of choice, but elbow macaroni or pipe rigate would work well too.
  • Three types of cheese – Gruyere, sharp cheddar, and pecorino or Parmesan! The nutty Gruyere and tangy cheddar melt beautifully into the creamy sauce. A little pecorino adds savory depth of flavor.
  • Shallots – You’ll roast them alongside the squash to add oniony flavor to the sauce.
  • Extra-virgin olive oil – It helps the squash blend into a creamy puree.
  • Balsamic vinegar, nutmeg, and ground sage – For fall flavor! The tangy vinegar and warm, earthy seasonings bring out the butternut squash taste.
  • Onion powder and garlic powder – For an umami kick.
  • Unsweetened almond milk – Feel free to use 2% or whole milk if you prefer.
  • Panko breadcrumbs – They create a delicious crispy topping for the comforting pasta.
  • And salt and pepper – To make all the flavors pop!

Find the complete recipe with measurements below.

Roasted butternut squash in a baking dish

How to Make Butternut Squash Mac and Cheese

You can find the full recipe with measurements and step-by-step instructions at the bottom of this post. But to get you started, here’s a quick overview of how it goes:

Start by roasting the squash and shallots. 

Tip: To get ahead, do this step in advance. You can store the roasted vegetables in an airtight container in the fridge for up to 4 days or freeze them for up to 3 months. Once they’re cooked, the rest of the recipe comes together quickly!

Meanwhile, prepare the topping by tossing the panko with a little olive oil, and cook the pasta. Before you drain the pasta, reserve 1 1/2 cups of the starchy cooking water.

Roasted squash, shallots, and spices in a blender

Next, make the squash puree. Measure 2 cups of the soft roasted butternut squash flesh. Add it to a blender with the shallots, olive oil, balsamic, salt, onion powder, garlic powder, sage, nutmeg, and several grinds of pepper.

Pouring pasta water into blender with sauce ingredients

Pour in the reserved pasta water…

Creamy butternut squash puree

…and blend until creamy.

Then, make the cheese sauce. Return the pasta pot to the stove, add the almond milk, and warm it over medium heat. Pour in the squash puree and cook, stirring often, until warmed through.

Whisking constantly, gradually add the cheeses, making sure each addition melts fully before adding the next.

Recipe Tip

Grate the cheese yourself! Store-bought shredded cheese is often coated in anti-caking agents, which can prevent it from melting into a smooth and creamy sauce.

Shell pasta in pot with cheese sauce

When all the cheese is melted and the sauce is creamy, add the cooked pasta. Stir to coat it in the luscious sauce.

Creamy butternut squash mac and cheese in pot with wooden spoon

Yum!!

Sprinkling panko topping over pasta in baking dish

Finally, bake the butternut mac and cheese. Transfer it to an oiled 9×13-inch or similar baking dish, and top with the panko. Broil until the topping is crisp and browned.

Let stand for 15 minutes before serving. Then, dig in!

Butternut squash mac and cheese in a baking dish next to two individual servings in bowls

Serving Suggestions

This butternut squash mac and cheese is such a cozy fall dinner! Pair it with a simple veggie side dish like steamed broccoli, roasted broccoli, or roasted Brussels sprouts. It also goes nicely with a fresh salad like one of these:

Another option: Serve the butternut mac and cheese as a Thanksgiving side dish! It’ll be a total crowd-pleaser.

Butternut squash mac and cheese recipe

More Recipes You’ll Love

If you love this butternut squash mac and cheese, try one of these Love & Lemons recipes next:

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Butternut Squash Mac and Cheese

rate this recipe:
4.84 from 50 votes
Prep Time: 20 minutes
Cook Time: 1 hour
Total Time: 1 hour 20 minutes
Serves 8
Creamy, cheesy, and SO delicious, this butternut squash mac and cheese is the ultimate fall comfort food. To get ahead, roast the squash and shallots up to 4 days in advance. Store them in an airtight container in the fridge until you're ready to make the pasta.

Ingredients

For the topping

Instructions

  • Preheat the oven to 425°F, line a baking sheet with parchment paper, and grease a 9x13-inch baking dish.
  • Slice the squash in half lengthwise and scoop out the seeds. Drizzle the cut sides with olive oil and sprinkle with salt and pepper. Place cut side down on the baking sheet. Place the shallots on a piece of foil, drizzle with olive oil and sprinkle with salt, and wrap tightly. Place on the baking sheet and roast for 30 to 45 minutes, or until the squash is soft.
  • Make the topping: In a small bowl, place the panko and olive oil. Toss to combine.
  • Bring a large pot of salted water to a boil. Prepare the pasta according to the package instructions, cooking until al dente. Reserve 1½ cups of the starchy pasta water before draining.
  • Measure 2 cups of the cooked, soft squash flesh and transfer to a blender with the 1½ cups pasta water, the shallots, olive oil, balsamic vinegar, salt, onion powder, garlic powder, sage, nutmeg, and several grinds of pepper. Blend until creamy.
  • Return the pasta pot to the stove and heat the almond milk over medium heat. Stir in the squash sauce and cook, stirring often, for 3 minutes, or until warmed through. Whisking constantly, gradually add the cheddar, Gruyere, and pecorino cheeses, making sure each addition is fully melted before adding the next. Whisk until all the cheese is fully melted and the sauce is creamy, then add the pasta and stir until coated.
  • Preheat the oven broiler and transfer the pasta to the prepared baking dish. Top with the panko and broil for 5 to 10 minutes, or until the topping is crisp and browned.
  • Let stand for 15 minutes before serving.

Notes

*To make this recipe gluten-free, use gluten-free pasta and gluten-free panko.
For a similar vegan recipe, I recommend making my creamy butternut squash pasta or vegan mac and cheese.

96 comments

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Rate this recipe (after making it)




  1. Jean Reuter
    10.31.2023

    I made the Butternut Squash Pasta and it was delicious. So many flavors. Served it over Protein Pasta. Love fall recipes!

    • Jeanine Donofrio
      10.31.2023

      I’m so glad you enjoyed it!

  2. Annika Carnes
    10.30.2023

    5 stars
    This butternut squash Mac & cheese is the absolute best! So tasty and you can’t even tell that one of the ingredients is butternut squash. My son who is convinced he doesn’t like butternut squash had two large servings because “it was soooo good!” That says it all.

    • Jeanine Donofrio
      10.31.2023

      Hi Annika, I’m so glad he loved it, ha!

  3. Samantha Barnett
    10.30.2023

    5 stars
    So, so good! We made this for Halloween but it may be on the menu again for Thanksgiving because it’s so good!! Used a nonstick pot to cook the pasta and sauce for easy clean up.

    • Jeanine Donofrio
      10.31.2023

      Hi Samantha, I’m so glad it was a hit!

  4. Monica
    10.30.2023

    5 stars
    This was so delicious and it was fun to be able to use fresh butternut squash straight from the garden!

    • Jeanine Donofrio
      10.31.2023

      I’m so glad you enjoyed it!

  5. Aurora Hernandez
    10.29.2023

    5 stars
    I will definitely be making this again I was up for this challenge. The last time I made Mac and cheese it didn’t come out so well. This was better than Trader Joe’s.

    • Jeanine Donofrio
      10.31.2023

      Hi Aurora, I’m so glad you loved it!

  6. Victoria Petty
    10.29.2023

    5 stars
    This recipe involved more prep and organizing skills but we (me and my grandaughter) were up for the challenge! It was fun and delicious, and a nice twist on standard Mac n cheese.. next time I might play around with different cheeses, just for the fun of it!

    • Jeanine Donofrio
      10.31.2023

      Hi Victoria, I’m so glad you both enjoyed making it!

  7. Laura
    10.29.2023

    Will the leftover cheese sauce freeze/reheat well?

    • Jeanine Donofrio
      10.31.2023

      Hi Laura, I haven’t tried so I’m not sure. It might separate or become grainy.

  8. Stefanie Vogt
    10.28.2023

    5 stars
    This was a delicious seasonal spin on one of my favourite foods! I don’t usually use Gruyère in mac and cheese, but it really complemented the squash. The sauce looked a bit too runny when I first mixed it with the pasta, but after baking and the recommended 15 minute rest, it thickened up nicely. I’ll definitely make this recipe again next fall!

    • Jeanine Donofrio
      10.31.2023

      I’m so glad you enjoyed it!

  9. Susan Collison
    10.27.2023

    4 stars
    It always amazes me how creamy of a sauce you can make from cashews & other great ingredients! I made the heart-healthy vegan mac & “cheese” recipe. My husband & I really appreciate your healthy vegan alternatives! Thank you, Janine! <3

    • Susan Collison
      10.28.2023

      *Jeanine ~ sorry!

  10. Markie Pringle
    10.27.2023

    5 stars
    I followed the recipe exactly and sprinkled smoked paprika on top before baking. Shared with friends and all of us loved it. Thank you.

    • Jeanine Donofrio
      10.27.2023

      Hi Markie, I’m so glad it was a hit!

  11. Christy Bragg
    10.26.2023

    5 stars
    Served this at my women’s Bible study and everyone loved it!!!

    • Jeanine Donofrio
      10.27.2023

      Hi Christy, I’m so glad it was a hit!

  12. Christy Bragg
    10.26.2023

    My picky adult son couldn’t even tell it had butternut squash in it. We all thought it was great.

    • Jeanine Donofrio
      10.27.2023

      Ha ha 🙂

  13. Chris
    10.26.2023

    Can we substitute trader Joe pre cut butternut squash instead of roasting a whole one

  14. Dawn Watson
    10.25.2023

    5 stars
    My first butternut squash endeavor and it was absolutely amazing and easy to do! Fed everyone at work and they said best mac and cheese ever!

    • Jeanine Donofrio
      10.27.2023

      I’m so glad it was such a hit!

  15. Adrienne Lamp
    10.25.2023

    5 stars
    So delicious! I love the sweetness from the squash and the crunch from the panko topping. I sprinkled a bit of smoked paprika over the crust for added flavor and color. I also find I can shave off a bit of roasting time by throwing the halves in the microwave for a few minutes and finishing them by roasting in the oven. It helps move things along a little without giving up flavor!

    • Jeanine Donofrio
      10.27.2023

      That’s a great tip, I’m glad you enjoyed the recipe!

  16. Aviella Strauss
    10.25.2023

    4 stars
    I actually loved making this as i haven’t made something like it before~ the squash came out very flavorful and the final dish was yummyy

    • Jeanine Donofrio
      10.27.2023

      I’m so glad you enjoyed it!

  17. Brenda Leis
    10.24.2023

    5 stars
    Great way to sneak an extra veggie in.

  18. Amanda Lewis
    10.23.2023

    5 stars
    Ny new favorite mac and cheese! We used gluten free noodles and they worked great in the recipe!

  19. Meagan Kivlighn
    10.22.2023

    5 stars
    My new fav Mac and cheese recipe! The perfect fall twist on a classic comfort food.

    • Jeanine Donofrio
      10.23.2023

      I’m so glad you loved it!

  20. JoAnne Baldwin
    10.22.2023

    4 stars
    Crispy Onions won over Pretzels for topping but the broil got a little toasty – next time I’ll tent it with foil from the get-go.

    I would have upped the spices (realized I forgot the nutmeg when I was two bites in), but the three cheese blend was tasty! Might take half of the roasted squash and chop it to stir into the pasta rather than purée it all to add some texture. Perfect fall comfort meal.

    • Jeanine Donofrio
      10.23.2023

      Hi JoAnne, I’m glad you enjoyed it!

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Photograph of Jeanine Donofrio and Jack Mathews in their kitchen

Hello, we're Jeanine and Jack.

We love to eat, travel, cook, and eat some more! We create & photograph vegetarian recipes from our home in Chicago, while our shiba pups eat the kale stems that fall on the kitchen floor.