Butternut Squash Mac and Cheese

One of my family's favorite frozen meals is Trader Joe's Butternut Squash Mac and Cheese, but if you know me, you know I like to avoid preparing frozen meals as much as possible. If it can be made from scratch, I want to make it from scratch!

That's where this recipe for Butternut Squash Mac and Cheese comes in. It's rich and creamy, and oh, wow, it is so flavorful! Complete with three types of cheese, a cozy blend of seasonings, and roasted butternut squash, it has everything you could possibly want in a creamy mac and cheese recipe.

After making it for the first time, I knew my family wouldn't be buying the boxed version anymore. It's homemade butternut squash macaroni and cheese from now on!

And if you want to make it vegan or gluten-free, that's easy. I'll show you how you can make this amazing mac and cheese any way you like!

two white bowls of butternut squash mac and cheese

Butternut Squash Mac and Cheese Ingredients

Butternut squash
Rigatoni pasta
Olive oil
Flaky salt
Milk
Dried thyme
Garlic powder
Cayenne powder
Nutmeg
Paprika
Dried rosemary
Additional salt to taste
Pepper
Butter
Bay leaf
Shredded cheddar cheese
Shredded mozzarella cheese
Panko breadcrumbs
Grated Parmesan cheese

It might seem like a lot of ingredients at a glance, but the ingredients for making homemade butternut squash mac and cheese are actually really simple: you just need squash, pasta, seasonings, cheese, milk, olive oil, breadcrumbs, and butter.

The star ingredient here is (of course!) the roasted butternut squash. You will not believe the nutty, warm flavor squash adds to mac and cheese that is so pleasing with a savory blend of cheese and seasonings.

butternut squash mac and cheese ingredients with labels

How to Make Butternut Squash Mac and Cheese

Roasting Butternut Squash

Preheat your oven to 400°F. While it's preheating, cut butternut squash in half. Place halved squash on a baking sheet and lightly drizzle oil over the top with a few pinches of flaky salt.
Then, place the baking sheet in the oven. Roast until soft, about 25 minutes. After removing it from the oven, let it cool slightly.

TIP: If you're not sure if it's ready, pierce the center of the squash with a fork. If it goes through easily and the squash is soft, it's done. If not, leave it in for a bit longer.

Making Mac and Cheese

Bring a large pot of salted water to a boil while your squash cools. You'll want to reserve some of that pasta water, so keep that in mind before draining later!
Scrape out squash with a spoon.
Add the squash to a blender with milk, thyme, paprika, garlic powder, cayenne powder, nutmeg, dried rosemary, salt, and pepper.
Blend until smooth and creamy.
Add pasta to the boiling water. Let it cook until al dente (just slightly underdone), then drain and reserve ½ cup of the pasta water.
Heat a large skillet over medium heat and melt butter.
Add a bay leaf to the skillet and saute for 2-3 minutes until fragrant. Remove the bay leaf.
Carefully add squash puree to the skillet to begin cooking it down.
Top with shredded cheddar and mozzarella and mix well until fully incorporated.
Simmer over low heat for 5-6 minutes. Add reserved pasta water if needed to thin it out.
While simmering, in a small bowl, combine breadcrumbs, Parmesan cheese, salt, and pepper. Set aside.
Add cooked noodles to the squash sauce and gently mix to combine.
Spoon squash mac and cheese into bowls for serving and evenly top with the breadcrumb mixture. Serve, and enjoy!

Butternut Squash Mac and Cheese Recipe Tips

Flaky sea salt is the absolute best salt to use for roasting vegetables. I highly recommend using a flaky salt like Maldon sea salt flakes to season the squash rather than regular table salt.
You can use your favorite type of pasta, but rigatoni is a great choice for coating with the mac and cheese sauce. It holds up very well to this dish.
Cheddar and mozzarella make a perfect cheese blend for this dish, but you can also use other cheeses like gruyere or even gouda, if you like.

a small white bowl of butternut squash mac and cheese

Vegan Butternut Squash Mac and Cheese

If you want to make your butternut squash mac and cheese vegan, all you have to do is swap (or leave out) a few ingredients in this recipe. Here are some ways to alter the recipe to be vegan:

Swap out the cheese for vegan shredded cheese if you like, or leave it out entirely. Instead of cheese, you can use 3 Tablespoons nutritional yeast, which will give it a cheesy flavor while keeping it vegan.
Swap out the butter for vegan butter.
Swap out the milk for vegan milk (any kind you like best).

Gluten-Free Butternut Squash Mac and Cheese

Making butternut squash mac and cheese gluten-free is a matter of replacing the pasta with your favorite gluten-free pasta, and the breadcrumbs with gluten-free breadcrumbs.

Squash Mac and Cheese FAQs

What does butternut squash mac and cheese taste like?

Butternut squash macaroni and cheese has a slightly nutty, autumnal flavor from the squash, while adding additional creaminess that complements the rich, cheesy sauce.

Can you freeze butternut squash mac and cheese?

Butternut squash mac and cheese is easy to freeze. Let it cool, then add it to tightly-wrapped freezer-safe containers and store for up to 3 months. Don't forget to label with the date! When you're ready to enjoy it again, add it to the oven at baking temperature for about 30-35 minutes until heated through.