Tuck roasted butternut squash puree into this delightful butternut squash mac and cheese casserole for color and flavor. Lots of sharp cheddar cheese plus salty parmesan balance the sweetness of the squash for a lovely vegetarian main dish. Easily made gluten-free if needed!

This butternut squash mac and cheese is a beautiful, sweet-and-salty recipe that I adapted from the NY Times. It's been a staple in my kitchen for years and makes a comforting, hearty winter meal. I love it on the holiday table (perhaps drizzled with a little vegetarian gravy and served alongside roasted cauliflower?), but it's welcome any night of the week. Kids like it, you'll have plenty of leftovers, and it's super cozy - what's not to love?!
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What You'll Love
- Quick and easy. This is a simple enough recipe, featuring butternut squash roasted, pureed, and folded into a cheese sauce that's then swirled with your choice of pasta and baked a little while longer. To save time, make the sauce and pasta while the squash roasts.
- Makes a ton! You'll get an enormous amount of mac here - a family of four could get about two dinners out of this recipe, which is super helpful when meal planning.
- Easy to make gluten-free. I've included instructions for making this dish gluten-free or not (spoiler: you'll just need to change out the type of pasta and flour depending on your needs. That's it!).
- Kid-friendly. This macaroni and cheese has a slight sweetness from the squash, and if your kids are anything like mine, they will LOVE that aspect and gobble it up. It's a nice way to add a little extra veg without being in their faces about it.

Ingredients Needed
Here's a quick look at what you'll need for this dish. Make sure to scroll down to my recipe card at the bottom of this post for the full ingredient amounts and instructions!
- Butternut squash
- Pasta - Use elbows or your favorite "nooks and crannies" pasta. For gluten-free, I love Jovial brand brown rice pasta, which works really well in baked pasta recipes.
- Butter - Use unsalted butter or non-dairy butter.
- Flour - If you don't need to keep gluten-free, use all-purpose flour. If you are making this recipe gluten-free, use sweet white rice flour, a starchy, glutinous gluten-free flour.
- Milk - I used a blend of whole milk and 2% milk. For more richness, you can use half-and-half, cream, or all whole milk.
- Cheddar cheese - I love really sharp cheddar cheese here, but you can use any variety you prefer. I shred my own cheese rather than buying pre-shredded cheese, which can include anti-caking agents.
- Mozzarella cheese - If needed, swap another cheese or use all cheddar if needed.
- Parmesan - A bit of shredded or grated parmesan sprinkled over the top adds a nice finishing touch.
- Salt and pepper

Step-by-Step Instructions
Here's an overview in photos of how to make butternut squash mac and cheese:

1. Make sauce: Start roasting the squash and cooking the pasta. Melt butter in a pot, add the flour, and then stir in the milk to form a thick sauce.

2. Add cheese: Mix in the cheese until it melts.

3. Combine: When the squash is done, puree it. Then fold in the pasta and the squash together with the cheese sauce.

4. Bake: Spread in a large pan, then place in a 350F oven and bake for about 30 minutes until the sauce is bubbly.

Tips & Recipe Notes
- Don't overcook the pasta. Follow the instructions on your box of pasta, then cook for about 1-2 minutes less time so that the pasta is al dente (slightly firm). It will soften in the oven as it bakes and soaks up the sauce.
- Rest after baking. Allow the baked mac and cheese to rest for about 5-10 minutes after it comes out of the oven so that it is not overly goopy.
- Try different pasta shapes. You can use any kind of pasta shape here, though I prefer tubed or shaped "nooks and crannies" pasta like penne, ziti, or macaroni.
- Add breadcrumbs. For a little crunch, mix 4 tablespoons of melted butter with ¼ cup of gluten-free or regular breadcrumbs, then scatter this mixture over the top of the pan. before baking.
- Different cheese. These are my favorite cheeses to use, but feel free to try others. Gruyere is nice, and Jack cheese will add a mellow smoothness.
- Try sweet potatoes! Swap the pureed butternut squash for about 1-2 cups of pureed sweet potatoes (depending on how much you want to add).
- Or a different squash. All winter squashes are lovely here - try acorn squash, kabocha, or even pumpkin!
Proper Storage
- Fridge - Transfer any cooled leftovers to an airtight container and store in the fridge for up to 3 days. I don't recommend freezing leftovers because the pasta can get mushy after defrosting.
- To Reheat - Place the leftover mac and cheese in an oven-safe dish and bake at 350F until warmed through, or place a portion on a microwave-safe plate or in a microwave-safe bowl and heat in the microwave for about 2 minutes until hot.

More Easy Pasta Recipes
Happy baking! If you make this butternut squash mac and cheese recipe, I'd love to know. Please leave a comment below, reach out with any questions, and tag me on Instagram @Cucina Nicolina ❤️
Recipe

Butternut Squash Mac and Cheese
Ingredients
- 1 butternut squash , medium sized
- 1 package pasta , gluten free if needed (such as elbows, penne, ziti, etc.)
- ¼ cup unsalted butter
- ¼ cup sweet white rice flour , or all-purpose flour (40 grams)
- 1 cup whole milk
- 1 ½ cups 2% milk
- 2 cups shredded cheddar cheese
- 1 cup shredded mozzarella cheese
- ½ teaspoon fine sea salt or to taste
- ½ teaspoon black pepper
- ½ cup shredded parmesan cheese
Instructions
- Preheat the oven to 375℉. Cut the 1 butternut squash in half and place it on a lined or greased baking sheet, cut side down. Roast for about 45 minutes, until fork-tender. Remove from the oven, cool slightly, then scoop out the cooked flesh. Puree until smooth. Set aside.
- While the squash is roasting, cook the 1 package pasta according to the package directions, then set aside in a large bowl.
- Turn the oven down to 350℉ and butter or grease a 9x13-inch baking pan.
- In a large saucepan over medium heat, melt the ¼ cup unsalted butter. Whisk in the ¼ cup sweet white rice flour and cook for about 2 minutes, whisking, until a paste forms. Whisk in the 1 cup whole milk, whisking constantly, until smooth, then whisk in the 1 ½ cups 2% milk until a smooth sauce forms. Cook, whisking often, until a thick sauce forms, about 5 minutes.
- Remove the sauce from the heat and stir in 1 cup of the 2 cups shredded cheddar cheese and ½ cup of the 1 cup shredded mozzarella cheese until melted. Stir in the ½ teaspoon ½ teaspoon fine sea saltand ½ teaspoon black pepper.
- Pour the cheese sauce onto the pasta in the bowl, and mix so that the pasta is coated with sauce. Stir in the pureed butternut squash. Spread half the pasta mixture in the prepared pan, then sprinkle with 1 cup of cheddar cheese and the remaining mozzarella cheese. Top with the remaining pasta mixture. Finish with the remaining ½ cup of cheddar cheese and sprinkle the top with ½ cup shredded parmesan cheese .
- Place in the oven and bake for about 20-30 minutes, until the cheese is melted and the sauce is bubbling. Remove from the oven and let rest for 5-10 minutes before serving.
Notes
- Don't overcook the pasta. Follow the instructions on your box of pasta, then cook for about 1-2 minutes less time so that the pasta is al dente (slightly firm). It will soften in the oven as it bakes and soaks up the sauce.
- Rest after baking. Allow the baked mac and cheese to rest for about 5-10 minutes after it comes out of the oven so that it is not overly goopy.
- Try different pasta shapes. You can use any kind of pasta shape here, though I prefer tubed or shaped "nooks and crannies" pasta like penne, ziti, or macaroni.
- Add breadcrumbs. For a little crunch, mix 4 tablespoons of melted butter with ¼ cup of gluten-free or regular breadcrumbs, then scatter this mixture over the top of the pan. before baking.
- Different cheese. These are my favorite cheeses to use, but feel free to try others. Gruyere is nice, and Jack cheese will add a mellow smoothness.
- Try sweet potatoes! Swap the pureed butternut squash for about 1-2 cups of pureed sweet potatoes (depending on how much you want to add).
- Or a different squash. All winter squashes are lovely here - try acorn squash, kabocha, or even pumpkin!
Nutrition
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Stephanie says
Thanks so much for this. I had a butternut squash searching for meaning and made this tonight following the NYT recipe. (I didn't have gruyere on hand) I halved the recipe, added a bit of salt and used half white and half yellow cheddar. Everyone cleaned their plates! They couldn't place the taste but finished it up. I had made earlier in the day and refrigerated, so I cooked at 400 for about 25 minutes. I had some leftover cheese sauce to which I added worcester sauce and dry mustard for welsh rarebit over toast for lunch. I had forgotten how much I loved that as a kid. This was a really nice change from straight up Mac and cheese (and snuck in some more veggies). The rest of the roasted butternut is going to find a home in pasta sauce later this week!
little kitchie says
i just love butternut squash in pasta dishes! and with lots of cheese... yum.
beautiful post! i hope you post those ginger cookies soon - those are our favorites!!
Art & Lemons says
Yowzer, this looks good! Is it wrong that I'm craving mac & cheese for breakfast now?
Lisa says
I'm feeling incredibly homesick for an evening with the 6 of us tucked into your living room drinking wine and playing board games. This mac 'n cheese would have been the perfect meal (for some of us).
sizzle says
YUM