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! 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 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.
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.
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.
Pour in the reserved pasta water…
…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.
When all the cheese is melted and the sauce is creamy, add the cooked pasta. Stir to coat it in the luscious sauce.
Yum!!
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!
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.
More Recipes You’ll Love
If you love this butternut squash mac and cheese, try one of these Love & Lemons recipes next:
- Homemade Mac and Cheese
- Vegan Mac and Cheese
- Cauliflower Mac and Cheese
- Butternut Squash Risotto
- Creamy Butternut Squash Pasta
- Butternut Squash Ravioli
- Butternut Squash Soup
Butternut Squash Mac and Cheese
Ingredients
- 1 large butternut squash
- 2 shallots, roughly chopped (⅔ cup)
- 1 pound shell pasta, or pipe rigate or elbows*
- ¼ cup extra-virgin olive oil, plus more for drizzling
- 2 teaspoons balsamic vinegar
- 1½ teaspoons sea salt
- 1 teaspoon onion powder
- ½ teaspoon garlic powder
- ½ teaspoon ground sage
- ¼ teaspoon nutmeg
- Freshly ground black pepper
- 1½ cups unsweetened almond milk
- 6 ounces grated sharp cheddar cheese, about 2½ cups
- 6 ounces grated Gruyere cheese, about 2½ cups
- 1½ ounces finely grated pecorino cheese, ½ cup
For the topping
- ¾ cup panko breadcrumbs*
- 1½ teaspoons extra-virgin olive oil
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.
10 min. of broil seems a little excessive. After 2 min. the top started to burn. Was still delicious!
Hi Marc, so sorry to hear that, broilers can vary so much! Glad you still enjoyed the recipe.
Without the cheese, the sauce was already absolutely delicious. The final dish was fantastic: home made comfort food at its best.
I’m so glad you enjoyed it!
I did a test run for thanksgiving and the flavor profile was delicious!! Personally, I loved the touch of balsamic vinegar. Two questions I could use help with:
1) The sauce was a little runny, and I ended up using a slotted spoon (small holes) to put the coated pasta into the baking dish. I was thinking of putting less pasta water in next time. That said, I did serve it right after making it and I wonder if it sat for a while if the sauce would thicken? What do folks think?
2) My blended squash & spices mixture turned brown because of the balsamic vinegar. How do the photos here look so bright orange? Is there some kind of not-as-brown balsamic that I should look for to retain the color?
Thank you!
A bit of a delayed response, but maybe someone will spot this and perhaps even have a reply or opinion they care to share. I am making this next week for a neighborhood gathering, this will be a test-drive for thanksgiving. On the basalmic, I have two options:
-Jalapeno balsamic (has a decent little kick)
-Cinnamon balsamic (warm cinnamon flavor without being overpowering)
Which do you think might be better in this recipe? A semi-pro cooking friend thought the jalapeno option might be the way to go, because it would lend a little kick* and diversity of flavor. But I am thinking the cinnamon is a natural with the other spices present in this recipe. There may be no wrong answer on this one, but I am curious what opinions you might have, dear foodie friends?
*I am also planning on caramelizing some fresh jalapeno rings to serve on the side as an optional for the neighborhood gathering. This may satisfy the need for a “kick” but it might also really enhance the jalapeno balsamic if that’s the way I go. Hm . . .
I’d go with jalapeno. There’s already nutmeg in this and I think the cinnamon would give it too much “pumpkin pie” vibe. The caramelized jalapenos sound like a great topper.
Let me know when it’s ready, I’ll be on my way ;-D
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.
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?
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.
I just made this and it’s in my fridge but I’m already worried about the balsamic. It doesn’t smell appetizing and I’m preparing a back up dish just in case.
Do you think it would have been good without the balsamic vinegar?
Hi Evelyn, we love the balsamic’s tangy flavor here, but you can feel free to skip it if you’d like! If you do use it, make sure you have a thin balsamic vinegar, not a thick balsamic glaze, which will have a more concentrated flavor.
Hi, I was thinking of making an extra batch and freezing it. Have you done this?
Hi Debbie, yes, it freezes well, the sauce is just a little more dry since it absorbs with the pasta longer. Still delicious.
If you do that it will cause the heat death of the universe so you probably shouldn’t.
Best
Todd
Hi!
I am wondering why you use almond milk vs a dairy product like whole milk. Excited to try this!
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!
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.
Hi Katie, without trying it, I’m not sure about replacing the pasta in this recipe. We have this Cauliflower Mac and Cheese recipe… it’s a bit different since it has a vegan sauce, but you might enjoy it: https://dailycove.info/cauliflower-mac-and-cheese/%3C/a%3E%3C/p%3E%3C/div%3E%3Cdiv class=reply>
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!
I’m so glad you loved it!
Wait, why do we heat over to 425? I didn’t see any baking instructions, just broil
Hi Claudia, you bake the butternut squash halves in the oven in step 2.
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?
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.
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!
I’m so glad you loved it!
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!
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.
I’m in love with this butternut mac and cheese! Really, that’s all that needs to be said! 😉
Ha, I’m so happy to hear that!