Butternut squash mac and cheese is a healthy(ish) fall comfort food. Pureed butternut squash is blended into the mac and cheese for some added nutrition and flavor. If you’re a mac and cheese fan try this for a weeknight dinner or make it as part of your weekend meal prepping. It also makes good leftovers, so you can use it for work lunches too.  


Roast the Butternut Squash

Start by roasting the butternut squash. 

  • Cut the top and bottom off the squash and then peel it (photo #2).
  • Cut the squash in half and use a spoon to scoop out the seeds (photo #3).
  • Dice the squash into 1-inch chunks (photo #4).
  • Spread the squash chunks evenly on a baking sheet and roast for 25 minutes at 400 degrees Fahrenheit. 


roast butternut squash



roasted squash



If you don’t want to use cheddar cheese you can use one or more of the following types of cheese:

  • Gruyere
  • Monterey jack
  • Gouda
  • Fontina
  • Havarti
  • Mozzarella
  • Parmesan

Use either freshly grated or pre-shredded cheese. Buying a block of cheese and shredding it yourself is usually a cheaper option, however, pre-shredded works too if you want to save time.  

cheese sauce



Any bite-sized shaped pasta can be used in mac and cheese. If you don’t want to use elbow macaroni try one of these:

  • Cavatappi 
  • Shells
  • Bowtie or farfalle
  • Ziti
  • Fusili

To make this gluten-free, use brown rice pasta, quinoa pasta, chickpea pasta, red lentil pasta, or any other gluten-free pasta. 

butternut mac and cheese


Butternut Squash Mac and Cheese Variations

You can easily sneak in some veggies or protein into your mac and cheese to make it an even more complete meal. Try one or more of these suggestions:

  • Leftover roasted vegetables
  • Diced tomato
  • Steamed broccoli
  • Green peas (heat up some frozen peas for a quick fiber and protein boost)
  • Diced chicken or ham
  • Ground beef

Store It 

Store any leftovers in individually portioned airtight containers and store in the fridge for up to 4 days.  


More Healthy Dinner Recipes to Try

Vegan Mac and Cheese

Chicken Enchilada Casserole

Ground Beef and Sweet Potato Skillet

Chicken Fajita Sheet Pan 

Thai Red Curry with Chicken

Veggie Lasagna


Butternut Squash Mac and Cheese

A fall twist on mac and cheese. Pureed roasted butternut squash gives this mac and cheese some added nutrition and flavor. Make it for an easy weeknight dinner or as part of your weekend meal prep.
Prep Time15 minutes
Cook Time40 minutes
Total Time55 minutes
Course: Main Course
Cuisine: American
Keyword: butternut, fall recipes, mac and cheese
Servings: 4
Author: Gabriella @ Nutritious Minimalist


  • 2 tsp cooking oil (avocado or olive oil)
  • 1 small butternut squash, peeled, seeded, and cut into 1-inch chunks (about 4 cups)
  • 8 oz. elbow macaroni (2 cups dried pasta)
  • 1 small yellow onion, chopped (about 1 cup)
  • 2 cloves garlic, minced
  • 1/2 tsp ground mustard
  • 1/2 tsp salt, more to taste
  • 1.5 cups shredded sharp cheddar cheese
  • 2.5 cups unsweetened almond milk


Roast the Butternut Squash

  • Preheat the oven to 400 degrees Fahrenheit. 
  • In a large bowl, toss the butternut squash chunks with 1 tsp of oil until all pieces are coated. Season with salt and pepper.
  • Spread the squash pieces evenly on a baking sheet and bake for 25 minutes until the pieces are tender. 
  • While the squash is roasting, cook the pasta according to package directions.

Make the Sauce

  • Heat 1 tsp of oil in a heavy-bottomed pot (like a Dutch oven) over medium-high heat. Add the onion and cook for 5 minutes until it starts to become translucent. Add the garlic, mustard powder, salt, and cook another 30 seconds. 
  • Turn the heat off and add 4 cups of roasted squash chunks to the pot with the onions. Then use an immersion blender to puree everything together. I use an immersion blender to minimize cleanup, but you can also puree everything in a food processor or high-speed blender and then transfer it back to the pot.
  • Turn the heat to low and add the cheese and almond milk. Stir slowly until the cheese melts and the mixture becomes smooth. 
  • Add the drained pasta to the sauce and stir to combine. If you want the sauce to have a thinner consistency, slowly add more almond milk until it reaches the desired consistency.

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