Butternut Squash Mac and Cheese
This butternut squash mac and cheese is the ultimate autumn dinner! It’s creamy and cheesy and filled with roasted butternut squash, a blend of gouda and cheddar cheeses, and both savory and sweet seasonings to make a super flavorful seasonal dish.

Elevate your mac and cheese this fall with this butternut squash mac and cheese recipe! It’s made with roasted butternut squash, both gouda and cheddar cheese, and lots of delicious autumn seasonings like sage, thyme, and nutmeg. The blended squash makes the cheese sauce extra creamy and smooth, and the herbs and spices give this mac and cheese a gorgeous seasonal flavor palate that makes it the perfect cozy fall meal! Whether you’re making a side dish for Thanksgiving or just an indulgent dinner this season, this butternut squash mac and cheese is sure to be a hit at any table.
Here are some more autumn pasta recipes you’ll love: Creamy Pumpkin Pasta Sauce, Pistachio Burrata Ravioli with White Wine Cream Sauce, and Gorgonzola Truffle Cream Sauce with Mushrooms.

Ingredients & Equipment
You’ll need the following ingredients and equipment to make this butternut squash mac and cheese:
- Large pot
- Baking sheet
- Immersion blender
- Pasta
- Butternut squash
- Shredded gouda
- Shredded cheddar
- Milk
- Butter
- Shallot
- Flour
- Olive oil
- Garlic powder
- Thyme
- Ground sage
- Nutmeg
- Salt and pepper
Customize This Recipe!
There are a few different ways you can customize this recipe:
- Have fun with spices. I love the sweet and savory blend of seasonings in this recipe, but you can adjust them a bit to tailor the dish more to your liking.
- Add protein. This pasta is delicious as-is, but you could totally add some sausage or bacon for a bit of extra flavor and protein!

Kitchen Tips:
- Utilize mise en place! Make sure you have all of your ingredients prepped and ready before you begin making this recipe – it will help save you time and keep you organized.
- Tips for melting in the cheese: to avoid clumping, turn the heat to the lowest setting (or remove the pot from heat completely), add the cheese in small handfuls, and whisk super well in between each handful to make sure the cheese is completely melted!
- Multitasking for efficiency: You can roast the squash ahead of time and wait for it to cool down slightly before starting your pasta and sauce, but if you want to save a bit of time, start boiling your pasta and making your sauce when the squash has about 5 minutes left in the oven. That way, when you take it out of the oven, it’ll be just about time to blend it into the sauce.
FAQ
I personally prefer using an immersion blender so you don’t have to use multiple dishes or equipment. You can simply scoop out the butternut squash from its skin, add it directly to the sauce, and blend it right in the pot so the whole sauce gets super smooth and creamy! If you don’t have an immersion blender, you can use a countertop blender or a food processor and blend the squash with a splash of milk to get it smooth, then whisk it into the rest of the sauce.
This butternut squash mac and cheese is best enjoyed directly after making, but it can be stored in a sealed container in the fridge for up to a week as well.

More pasta and sauce recipes:
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Butternut Squash Mac and Cheese
Ingredients
- 1 butternut squash
- 2 tbsp olive oil
- 1 pinch salt
- 1 pinch pepper
- 6 servings pasta according to package
- 3 tbsp butter
- 1 small shallot finely chopped
- 3 tbsp flour
- 1¾ cups milk
- 1 tsp salt
- 1 tsp pepper
- ½ tsp garlic powder
- ½ tsp sage
- ½ tsp thyme
- ½ tsp nutmeg
- 4 oz shredded cheddar
- 4 oz shredded gouda
Instructions
- Preheat the oven to 400ºF and prepare a baking sheet with parchment paper or til foil.
- Cut off each end of your squash, then slice it down the middle lengthwise, scooping out the seeds.
- In a small bowl mix the olive oil, salt, and pepper, then brush the mixture over the insides of the squash.
- Place both halves of the squash on the baking sheet open side down, then bake the squash for about 35 minutes or until tender and easily scooped. Set aside until use.
- With about 5 minutes left on the squash, boil a pot of water and cook the pasta until al dente according to package directions. Save ¼ cup of pasta water before draining.
- While cooking the pasta, add the butter and shallot to a large pot or saucepan and melt on medium-low heat until fragrant, about 1-2 minutes. Add the flour and whisk into the melted butter to form a roux, cooking for another 1-2 minutes.
- Slowly pour in the milk and whisk it into the roux until smooth. Mix in the salt, pepper, garlic powder, sage, thyme, and nutmeg and simmer for about 5 minutes to thicken the sauce.
- Remove the pot from the heat and slowly whisk in the cheese in handfuls until fully melted and smooth.
- Scoop the roasted squash directly into the pot/pan and blend with an immersion blender until fully smooth. You can also add the squash to a food processor with a splash of milk or water and blend until smooth, then pour into the cheese sauce and whisk until combined.
- Return the pot/pan to low heat and whisk ¼ cup of pasta water into the sauce. Stir in the cooked pasta until fully coated and heat for a few minutes, then transfer to a serving bowl and enjoy!
Notes
- Utilize mise en place! Make sure you have all of your ingredients prepped and ready before you begin making this recipe – it will help save you time and keep you organized.
- Tips for melting in the cheese: to avoid clumping, turn the heat to the lowest setting (or remove the pot from heat completely), add the cheese in small handfuls, and whisk super well in between each handful to make sure the cheese is completely melted!
- Multitasking for efficiency: You can roast the squash ahead of time and wait for it to cool down slightly before starting your pasta and sauce, but if you want to save a bit of time, start boiling your pasta and making your sauce when the squash has about 5 minutes left in the oven. That way, when you take it out of the oven, it’ll be just about time to blend it into the sauce.
- Have fun with spices. I love the sweet and savory blend of seasonings in this recipe, but you can adjust them a bit to tailor the dish more to your liking.
- Add protein. This pasta is delicious as-is, but you could totally add some sausage or bacon for a bit of extra flavor and protein!
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