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


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:
4.87 from 58 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.


For the topping


  • 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.


*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.


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Rate this recipe (after making it)

  1. Donna

    5 stars
    I made the dish for dinner tonight and everyone enjoyed it. I followed the recipe except for the milk. I used unsweetened soy milk as that is what we had on hand. I was worried the sauce was to runny, but it really thickened up while it sat after taking it out of the oven.

  2. Stephanie

    I just made this for the first time as a test run for Christmas. I worry about traveling and making this in my mother’s kitchen. Can I make the sauce ahead of time, and just make the pasta, incorporate the cheese, and broil the breadcrumbs on day of? Any thoughts on why that might not work?

  3. Lalanie O

    1 star
    Unfortunately my family did not enjoy this recipe. I feel like the balsamic vinegar completely ruined the recipe, but that’s just my flavor preference.

  4. Debbie

    Hi, I was thinking of making an extra batch and freezing it. Have you done this?

    • Jeanine Donofrio

      Hi Debbie, yes, it freezes well, the sauce is just a little more dry since it absorbs with the pasta longer. Still delicious.

  5. Cammie

    I am wondering why you use almond milk vs a dairy product like whole milk. Excited to try this!

    • Phoebe Moore (L&L Recipe Developer)

      Hi Cammie, we use unsweetened almond milk in all our recipes; it’s what we keep on hand in the kitchen. But if you prefer, you can totally use regular milk here. I’ve made it with 2%, and it came out delicious!

  6. Katie

    This sounds so good. I’m wondering what might happen if I made it with lightly cooked cauliflower and white beans instead of pasta. Do you think the cauliflower would release too much water during the broiling phase? I was thinking it could be a great addition for us vegetarians at the Thanksgiving table, knowing there will already be a lot of other starchy foods.

  7. Sally Dee

    5 stars
    Delicious! The instructions are straight forward and this was easy to put together after work. I have a lot of butternut squash and this recipe was a real treat!

    • Jeanine Donofrio

      I’m so glad you loved it!

  8. Claudia

    Wait, why do we heat over to 425? I didn’t see any baking instructions, just broil

    • Jeanine Donofrio

      Hi Claudia, you bake the butternut squash halves in the oven in step 2.

  9. Allegra

    Hi! This looks delicious! If making ahead for Thanksgiving, could I store the pasta and sauce mixed in the fridge, and then bake with panko the day-of?

    • Jeanine Donofrio

      Hi Allegra, I think that would work – it’ll just be a bit more dry because the pasta will soak up more of the sauce.

  10. Sonia

    Delicious – a fun recipe for fall! For someone whose not very adventurous withhold autumn squashes and cheese that’s not pre-shredded, it was definitely a labor of love but it was an experience and an ultimate comfort food!

    • Jeanine Donofrio

      I’m so glad you loved it!

  11. Sonia

    So delicious – the ultimate comfort food, for someone who’s not an adventurous cook, the recipe is definitely a labor of love but a balanced fun recipe for the season. I wish I added a spice element (either oregano or crushed red pepper but that’s a personal preference)… nothing tapatio can’t handle though!

  12. Erin Dominy

    5 stars
    We loved this! I could eat the butternut squash purée with its spices and balsamic vinegar by the spoonful, but add cheese and pasta and it’s amazing. Great with a kale salad, as suggested. Leftovers were gussied up with a drizzle of balsamic glaze, so good.

  13. Laurie Bettini

    5 stars
    I’m in love with this butternut mac and cheese! Really, that’s all that needs to be said! 😉

    • Jeanine Donofrio

      Ha, I’m so happy to hear that!

A food blog with fresh, zesty recipes.
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.