Easy Butternut Squash Mac and Cheese (oven baked)

5.0 from 53 votes

This is the best butternut squash baked mac and cheese recipe that you will ever taste! The combination of the creamy cheese sauce, tender macaroni, and sweet butternut squash is simply perfection. Trust me, once you try this dish, you will be hooked!

Fall is synonymous with everything pumpkin! More savory butternut squash dishes not to miss include oven baked chicken thighs with butternut squash, easy butternut squash gratin, butternut squash apple and sweet potato bake, or crunchy pumpkin croquettes!

Truly the best Homemade Mac & Cheese You’ve Ever Had!

This pumpkin mac and cheese is insanely cheesy, ultra-creamy, and topped with a crispy Panko topping. To make the ultimate macaroni and cheese, I used three kinds of cheese plus a homemade creamy sauce. 

Butternut Squash Mac and Cheese is an excellent option for picky eaters. The creamy sauce and nutty flavors are sure to please the entire family. So be sure to try this recipe next time you’re looking for a comforting meal!

This easy baked pumpkin mac and cheese recipe is perfect for fall when butternut squash is in season. Butternut squash is a type of winter squash that is popular in many dishes, including soups – one of my all time favorite is Pumpkin and Fennel soup, casseroles, and breads.

It can also be puréed and used as a replacement for pumpkin in pies or perfect fluffy Pumpkin Pancakes. Butternut squash has a sweet, nutty flavor that is similar to pumpkin. It is high in vitamins A and C, potassium, and fiber. It is a good source of magnesium, phosphorus, zinc, and calcium.

There are many ways to cook butternut squash. It can be roasted, baked, puréed, or added to soups and stews. When cooking with butternut squash, it is important to keep in mind that it takes longer to cook than other types of winter squash.

This recipe for butternut squash baked mac and cheese combines the sweetness of butternut squash with the creaminess of cheese for a delicious and easy-to-make dish.

The pasta is baked in a cheesy sauce together with butternut squash purée, milk, and mozzarella and cheddar cheese. It is then topped with more cheese and crispy Panko crumbs and baked until golden brown and bubbly.

Check out how to make it below, and don’t miss my PRO tips, I have everything you need to know as far as what cheeses to use, substitution ideas, variations of this recipe, and more!

• Elbow Macaroni – you can also use another type of tubular pasta if you like

• Butter – you can use unsalted or salted butter, whatever is handy

• Butternut Squash – medium sized one, we are going to use only half of it

• Mozzarella Cheese – shredded

• Cheddar Cheese – freshly grated or shredded

• Garlic Cloves

• Paprika – regular, or you can use smoked if you like.

• Cinnamon – this complements the butternut squash flavors very well, similar to sweet potato + cinnamon combination

• Rosemary – a fresh sprig works best.

• Flour – all-purpose or your favorite gluten-free blend.

• Milk – whole milk or plant-based, if you’re looking for a vegan option.

Toppings

• Panko Breadcrumbs
• Mozzarella Cheese – fresh or shredded.
• Parmesan – grated. To add even more flavor to my homemade butternut squash pasta, I add Parmesan to the Panko topping – so good!
• Pistachio – optional for garnish
• Rosemary – optional for garnish

See recipe card below this post for ingredient quantities and full instructions.

Start by preparing the butternut squash puree. We only need half of the squash, so you can save the other half for a later recipe (wrapped in foil, place it in the fridge)

Peel off the squash and cut it into large bite-sized pieces and boil them in a large pot of salted water for about 10-15 minutes until it has softened. When fork tender, drain ad transfer squash to a blender. Set aside.

Prepare the elbow macaroni pasta by boiling it in a large saucepan, according to package directions, less 1 minute. Cooking your pasta to slightly less than al dente, about one minute shy is perfect because the pasta will continue to cook in the homemade cheese sauce in the oven. You don’t want mushy macaroni.

Drain and then drizzle pasta with a bit of olive oil and stir to coat pasta. Set aside to cool while preparing cheese sauce.

Make the cheese sauce for baked mac and cheese.

Heat butter in a large skillet, over medium-high heat, add minced garlic along with the rosemary to infuse the flavor of the rosemary into the butter. Once the garlic has begun to turn slightly golden, add in the flour continue whisking for about 1 minute until bubbly and golden.

Gradually whisk in the milk until nice and smooth. Continue whisking until you see bubbles on the surface and then continue cooking and whisking for another 2 minutes. Add mozzarella and cheddar cheese, and whisk until smooth.

The sauce should be creamy and thick at this point. Season with salt and pepper and add cinnamon, and paprika to the mixture too.

Remove pot from heat and stir in the blended/ mashed butternut puree and whisk to combine well.

Stir in the cheesy pumpkin sauce, cooled pasta until combined and pasta is fully coated with the cheese sauce.

Pour the mac and cheese into prepared baking dish (lightly greased 9” x 11” baking dish) and set aside. Top the mac and cheese with the additional cheese and panko breadcrumbs. Bake in the oven, on the middle rack, until the top is lightly golden, about 25 minutes. Serve immediately.

Leftover mac and cheese can be stored in an airtight container in the fridge for up to 4 days. Then, reheat in the oven or microwave when ready to eat.

You can freeze leftover mac and cheese for up to 3 months. Then, thaw in the fridge overnight before reheating.

• If you are using fresh butternut squash and have some spare time, you can roast it in the oven before adding it to the mac and cheese. This will give it a slight sweetness and earthy flavor that goes well with the cheesy dish.

• Cook your pasta to slightly less than al dente, about one minute less then what they recommend on package instructions is perfect. The reason is that this is baked mac and cheese so the pasta will continue to cook in the homemade cheese sauce in the oven. You don’t want mushy macaroni.

• I used elbow pasta but really, any tubular pasta will work, as it will coat perfectly with the creamy sauce.

• If you want a creamier mac and cheese, you can add in some heavy cream or additional milk when you are reheating it.

• If the sauce is too thick, you can thin it out with a little water or additional milk.

• Butternut squash can vary in size, so you may need to adjust the amount of puree you use depending on how large your squash is.

• Use white cheddar cheese, instead of sharp cheddar cheese, for a more mild flavor

• You can use any kind of pasta you like for this recipe. We prefer elbow macaroni, but pasta shell or even fusilli are a great option too.

• If you want a dairy-free version of this mac and cheese, you can substitute the milk and cheese for plant-based alternatives. You can use unsweetened almond milk and vegan cheese, but other options like cashew milk or coconut milk would work well too.

• For some extra veggies, you serve your mac and cheese with some roasted Brussels sprouts, green beans, or even sweet potatoes.

• This recipe can easily be made gluten-free by using gluten-free pasta and omitting the breadcrumbs on top or using gluten-free bread crumbs instead.

• Add some extra spices like sage or garlic powder to the squash mixture for some extra flavor.

My favorite combination is Mozzarella and Sharp Cheddar for the sauce and definitely using delicious Parmesan on top of your mac & cheese dish. Your favorite macaroni recipes get a lift from the nutty undertones from these cheeses.

In order to add golden color to mac and cheese before baking, parmesan cheese is also perfect for grating on top. You can also use Gruyere cheese or smoked Gouda, if preferred.

NO, you don’t cover it with foil while baking to prevent having all that moisture inside. no one likes soggy, watery mac and cheese!

Butternut squash mac and cheese is a delicious, easy-to-make dish that the whole family will love. This recipe can be made with fresh or leftover butternut squash, and it’s perfect for fall flavors.

You can customize your mac and cheese with different cheeses and add-ins, like shredded chicken, bacon, or roasted veggies. This dish is also relatively healthy, thanks to the addition of butternut squash. So if you’re looking for a comfort food that’s not too heavy, this is it!

Butternut squash mac and cheese can be served as a main dish or side dish. It’s perfect for a weeknight meal or holiday dinner. And leftovers reheat well, so you can enjoy it for days afterward.

So what are you waiting for? Try this butternut squash mac and cheese simple recipe tonight!