Butternut Squash Mac and Cheese

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This butternut squash mac and cheese is creamy, cheesy and has butternut squash blended in the sauce for added nutrition and flavor. It’s easy to make in under 30 minutes – you can even save time and energy by using frozen butternut squash (instead of peeling and cutting fresh squash).  

a bowl of Butternut Squash Mac and Cheese garnished with fresh herbs


During my last pregnancy I created so many easy dinner recipes that have become family favorites (like these Greek meatballs, homemade chicken nuggets, etc), and this butternut squash mac and cheese might be the best of them all.

I took everything I love about our easy mac and cheese recipe and used it to create this butternut squash version. It is creamy, cheesy and has butternut squash blended in the sauce for added nutrition and flavor. Half of my kids like this version even better than “plain mac and cheese,” which is a huge compliment.

Plus, this recipe is easy to make in under 30 minutes – and you can even save time and energy by using frozen butternut squash (instead of peeling and cutting fresh squash).  Because we can use frozen squash, we make this a few times a month all year long!

Butternut Squash Mac and Cheese in a pan after it has been cooked garnished with fresh herbs

Butternut squash mac and cheese: Ingredients & substitutions

photo of the ingredients in this Butternut Squash Mac and Cheese recipe
  • Pasta. I have used just about every noodle variety to make this butternut mac and cheese recipe and it always turns out delicious! This wagon wheel pasta is my all-time favorite, and I buy it just to make this recipe. I do recommend a shape (macaroni of course, bowties, rotini, etc.) instead of spaghetti noodles, but they do work if it’s all you have! You can also use gluten-free pasta, whole wheat pasta, chickpea pasta, etc. etc. 
  • Butternut squash. You can either use butternut squash that has been peeled, deseeded and finely chopped or a bag of frozen squash (16 oz).
  • Salted Butter. There really isn’t a substitute for butter in this recipe. However you can use either salter or unsalted with great results.
  • All-Purpose Flour. There are a few substitutions that work well for the flour including corn starch, tapioca starch/flour, and all-purpose gluten-free flour.
  • Whole Milk. Any kind of liquid dairy works well in this recipe. Just remember the higher the fat content, the creamier your butternut squash mac and cheese will be (so I do not recommend using fat-free milk). 2% milk, whole milk, half and half and cream all work well! My favorite is whole milk.
  • Cheese.The quality of the cheese that you user really matters. If you wouldn’t eat it by itself, then don’t use it to make mac and cheese! I recommend a high-quality medium to sharp cheddar cheese, shredded gouda, or gruyere (or a combination of any of these) for the best flavor.
  • Salt & Pepper. Add these ingredients to taste! 
  • Minced garlic. you can substitute 1/4 tsp garlic powder for the minced garlic, or leave it out.
  • Onion. I don’t recommend omitting the onion as the flavor is really important. I suggest using a white or yellow sweet onion.
a bowl of Butternut Squash Mac and Cheese garnished with fresh herbs

How to make Butternut Squash Mac and Cheese

We’ll walk through this recipe step-by-step, and don’t forget to watch the video.

Begin this recipe by cooking the pasta in salted water, then drain it and set it aside but do not rinse.

cooked wagon wheel pasta in a strainer to be used in this Butternut Squash Mac and Cheese recipe

Next, add 2 tablespoons of butter, the butternut squash, onion and garlic to a large pot cover and cook over medium high heat until the squash is soft (about 10 minutes)

Frozen squash cooks faster than fresh. To make the squash cook faster you can cut it into very small pieces (dice it). You can also roast the squash in the oven if you prefer.

two photos showing How to Make Butternut Squash Mac and Cheese - cooking the onions and squash

Transfer the cooked butternut squash mixture to the container of a Vitamix, then add 1 cup milk and blend until smooth.

two photos showing How to Make Butternut Squash Mac and Cheese - blending the milk and cooked squash

In the pot, add the remaining 2 tablespoons butter and melt over medium heat.

Then, add the flour and sea salt and whisk until combined. Cook the flour mixture until it’s bubbling.

two photos showing How to Make Butternut Squash Mac and Cheese - making a roux to thicken the sauce

Next, add the remaining 1 cup of milk and whisk to combine. When the mixture is smooth, add the butternut squash mixture and whisk until smooth.

two photos showing How to Make Butternut Squash Mac and Cheese sauce

Cook over medium heat until it begins to thicken, once it has slightly thickened, whisk in the cheese until melted.

Then, add the cooked pasta to the cheese sauce, stir and serve.

two photos showing How to Make Butternut Squash Mac and Cheese sauce and adding the pasta

Serve

We enjoy this butternut mac and cheese often with a side salad (like this kale salad or brussel sprout salad), roasted broccoli, roasted brussel sprouts, and with some crusty bread like this no knead bread or pretzel bread.

I enjoy eating the leftovers for lunch for a few days, too!

Butternut Squash Mac and Cheese being served out of a pot

Store/freeze

Store the leftovers of this butternut mac and cheese in an airtight container in the refrigerator for up to 5 days or in the freezer for up to 2 months. It will thicken as it cools, but will thin out again when it’s reheated.

a fork taking a bite of Butternut Squash Mac and Cheese

Recipe FAQS

What cheeses go well together for mac and cheese?

My favorite is a mixture of sharp cheddar and gouda cheese. There are so many possibilities – gruyere, cream cheese, pepper Jack, Colby jack, cheddar, etc.

Can I double this recipe?

Yes, you can easily double this recipe to feed a crowd.

Can you freeze butternut mac and cheese?

Yes, store leftovers in the freezer in an airtight container for up to 2 months. Reheat in the microwave or oven set to warm.

What other mac and cheese recipes can I make?

Easy homemade mac and cheese is ready in 15 minutes!
This baked mac and cheese is so good!
Add some nutrition and make this Vegetable Mac and Cheese!
Try these baked mac and cheese cups!
For a low-carb version, try this spaghetti squash mac and cheese!

a bowl of Butternut Squash Mac and Cheese with a fork in it

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Butternut Squash Mac and Cheese

Laura
This butternut squash mac and cheese is creamy, cheesy and has butternut squash blended in the sauce for added nutrition and flavor. It’s easy to make in under 30 minutes – you can even save time and energy by using frozen butternut squash (instead of peeling and cutting fresh squash).
5 from 4 votes
Course Main Course, Side Dish
Cuisine American
Servings 12 Servings
Calories 308
Prep Time15 minutes
Cook Time25 minutes
Total Time40 minutes

Ingredients  

  • 16 oz pasta uncooked (macaroni, wagon wheels, shells, etc).
  • 1 lb. butternut squash peeled and finely diced, or use frozen squash
  • 4 TBS salted butter divided
  • ½ cup onion finely diced
  • 1 tsp minced garlic
  • 2 cups whole milk divided
  • 2 TBS all-purpose flour
  • ½ to 1 tsp sea salt
  • 12 oz shredded cheese (3 cups) sharp cheddar, gouda, gruyere, etc.

Instructions 

  • Cook pasta in salted water. Drain and set aside.
  • Next, add 2 tablespoons of butter, the butternut squash, onion and garlic to a large pot cover and cook over medium high heat until the squash is soft (about 10 minutes)
  • Transfer butternut squash mixture to the container of a Vitamix.
  • Add 1 cup milk and blend until smooth.
  • In the pot, add the remaining 2 tablespoons butter and melt over medium heat.
  • Add flour and sea salt and whisk until combined. Cook the flour mixture until it’s bubbling.
  • Then, add the remaining 1 cup of milk and whisk to combine.
  • Add the butternut squash mixture and whisk until smooth.
  • Cook over medium heat until it begins to thicken.
  • Once it has slightly thickened, whisk in the cheese until melted.
  • Add cooked pasta to the cheese sauce, stir and serve.

Video

Notes

*Frozen squash cooks faster than fresh. To make the squash cook faster you can cut it into very small pieces (dice it). You can also roast the squash in the oven if you prefer. 

Ingredient Substitutions

  • Pasta. I have used just about every noodle variety to make this butternut mac and cheese recipe and it always turns out delicious! This wagon wheel pasta is my all-time favorite, and I buy it just to make this recipe. I do recommend a shape (macaroni of course, bowties, rotini, etc.) instead of spaghetti noodles, but they do work if it’s all you have! You can also use gluten-free pasta, whole wheat pasta, chickpea pasta, etc. etc. 
  • Butternut squash. You can either use butternut squash that has been peeled, deseeded and finely chopped or a bag of frozen squash (16 oz).
  • Salted Butter. There really isn’t a substitute for butter in this recipe. However you can use either salter or unsalted with great results.
  • All-Purpose Flour. There are a few substitutions that work well for the flour including corn starch, tapioca starch/flour, and all-purpose gluten-free flour.
  • Whole Milk. Any kind of liquid dairy works well in this recipe. Just remember the higher the fat content, the creamier your butternut squash mac and cheese will be (so I do not recommend using fat-free milk). 2% milk, whole milk, half and half and cream all work well! My favorite is whole milk.
  • Cheese.The quality of the cheese that you user really matters. If you wouldn’t eat it by itself, then don’t use it to make mac and cheese! I recommend a high-quality medium to sharp cheddar cheese, shredded gouda, or gruyere (or a combination of any of these) for the best flavor.
  • Salt & Pepper. Add these ingredients to taste! 
  • Minced garlic. you can substitute 1/4 tsp garlic powder for the minced garlic, or leave it out.
  • Onion. I don’t recommend omitting the onion as the flavor is really important. I suggest using a white or yellow sweet onion.

Store/freeze

Store the leftovers of this butternut mac and cheese in an airtight container in the refrigerator for up to 5 days or in the freezer for up to 2 months. It will thicken as it cools, but will thin out again when you reheat it.

Nutrition

Serving: 0.75cup | Calories: 308kcal | Carbohydrates: 37g | Protein: 13g | Fat: 12g | Saturated Fat: 7g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 3g | Trans Fat: 0.2g | Cholesterol: 37mg | Sodium: 324mg | Potassium: 314mg | Fiber: 2g | Sugar: 4g | Vitamin A: 4392IU | Vitamin C: 9mg | Calcium: 223mg | Iron: 1mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Did you enjoy this recipe? Have a question? Leave a comment below!

Photos in this post were taken by Jamie from Dishing Out Health.

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Recipe Rating




5 Comments

  1. 5 stars
    Made this last night and everyone enjoyed it even my son who doesn’t like eating vegetables. So I approve for kids who don’t like eating their vegetables or are picky eaters.

    1. It feeds our family of 8 twice – but we have young kids eating (ages 12-2). I’d say it makes at least 10 servings.