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Butternut Squash Mac and Cheese

Butternut squash mac and cheese is just as creamy and cheesy as the original, but it sneaks in some extra nutrition thanks to the addition of everyone’s favorite winter squash!

Overhead view of butternut squash mac and cheese in bowl with fork

I always love the idea of mac and cheese, but a few bites in and I start to feel bloated and weighed down. All that dairy! All that cheese! Plus pasta! It’s a lot, right?

Butternut squash mac and cheese cuts some of that richness with the unlikely addition of roasted butternut squash. It’s a delicious twist on the classic comfort food and a flavorful, nutritious meal sure to please everyone at the dinner table.

(For more crowd-pleasing comfort food remakes, see my Lightened Up Broccoli Casserole and Creamy Mushroom & Wild Rice Soup.) 

The squash adds a slight nutty, sweet flavor and provides extra vegetables in every bite—but the sauce is still as cheesy and creamy as you want it to be. In fact, butternut squash mac and cheese might just be magic!

Overhead view of two bowls of butternut squash mac and cheese

Why You’ll Love This Butternut Squash Mac and Cheese Recipe

Here are some of the reasons this butternut squash mac and cheese is a guaranteed winner:

  • Creamy and perfect. The cheese sauce is silky smooth and ultra creamy without being heavy. You have to try it to see what I mean!
  • Versatile. Add some spinach or tempeh bacon, or try my vegan butternut squash mac and cheese variation below. Options: you have them!
  • Nutritious. Butternut squash is packed with vitamins, minerals, and antioxidants, making this dish a healthier twist on classic mac and cheese.
Overhead view of ingredients for butternut squash mac and cheese

What You’ll Need

Here are all of the ingredients you’ll need when making butternut squash mac and cheese. Make sure to check out the recipe card at the bottom of the page to see the exact quantities for each ingredient.

  • Butternut squash – Butternut is perfect for this recipe thanks to its mildly sweet flavor and vivid (cheese-like!) color.
  • Pasta – I recommend using a shape that will hold the cheese sauce well, like macaroni, rotini, or shells.
  • Olive oil 
  • Garlic
  • Shallot – If you can’t find shallots, yellow onions are the closest substitute.
  • Whole milk – Full-fat whole milk is necessary for a rich, creamy sauce.
  • Cheddar cheese
  • Parmesan cheese – Shelf-stable Parmesan (the kind that comes in the green plastic bottles) doesn’t melt well, so I recommend buying a wedge or block and grating it yourself.
  • Garlic powder
  • Onion powder
  • Salt and pepper

Should You Grate Your Own Cheese for Mac and Cheese?

Absolutely! Bagged shredded cheese has ingredients added to keep it from clumping; these ingredients also affect how it melts. You’ll end up with a smoother cheese sauce if you grate your own cheese.

How to Make Butternut Squash Mac and Cheese

If you want to get a head start on this recipe, you can roast the squash up to 3 days ahead of time.

  • Roast the squash. Halve the squash and scoop out the seeds. Brush with oil and bake at 350ºF for 30 to 40 minutes, or until fork-tender. 
  • Scoop the flesh. Once the squash is cool enough to handle, scoop out a pound of the flesh. (You can freeze any extras for another recipe.)
  • Cook the pasta. Follow the package directions and cook it to al dente.
  • Sauté the aromatics. While the pasta is cooking, heat a tablespoon of olive oil in a small saucepan. Add the garlic and shallot and cook over medium heat for 1 minute, or until fragrant.
  • Finish the sauce. Stir in the milk, cheddar, half of the Parmesan, squash, spices, and salt. Blend with an immersion blender until smooth, then season to taste.

Add the pasta and serve. Stir in the pasta and top with grated Parmesan cheese and basil, if desired.

Tips for Success

These hints and tips will help you make the best butternut squash mac and cheese:

  • Fully cook the squash. Make sure the butternut squash is fork-tender before you pull it out of the oven and use it in the sauce. It’s even better if it caramelizes a bit on the edges.
  • No immersion blender? No problem! If you don’t have an immersion blender, heat the milk with the oil and garlic and then pour it into a blender with the cheese, squash, spices and salt. Puree until smooth, but leave the lid partially open for venting and place a towel over the top to catch any splatters.
  • Don’t overcook the pasta. If you do, it will fall apart when you stir it into the butternut cheese sauce. This is especially true if you use a gluten-free bean- or lentil-based pasta.
Overhead view of butternut mac and cheese in Dutch oven with wooden spoon

Variations

You can swap in another variety of winter squash with a similar flavor profile, like honeynut, buttercup, or Hubbard. I also like this recipe with fresh rosemary, thyme, or sage leaves instead of basil.  

Serving Suggestions

Round out your dinner with a vegetable side dish like my Roasted Winter Vegetables with Maple Glaze. Another option is to pair your butternut squash mac and cheese with a salad; my Autumn Chopped Quinoa Salad with Apple Cider + Tahini-Sage Dressing would be perfect.

Bowl of butternut squash mac and cheese garnished with parmesan and sprig of basil

How to Store Leftovers

Leftover butternut squash mac and cheese can be stored in an airtight container in the refrigerator for up to 4 days. Reheat leftovers on the stovetop or in the microwave until heated through. If you find that the sauce has become too thick, add a splash of milk while reheating to thin it out. 

Can I Freeze This Recipe?

This recipe can be frozen for up to 3 months. Simply transfer the mac and cheese to a freezer-safe container or freezer bag before freezing. When ready to use, thaw it in the refrigerator before reheating it according to the instructions above.

Fork lifting butternut squash mac and cheese from bowl

More Cozy Winter Squash Recipes

Butternut Squash Mac and Cheese

Butternut squash mac and cheese is just as creamy and cheesy as the original, but it sneaks in some extra nutrition thanks to the addition of everyone’s favorite winter squash!
author: Alyssa
yield: 4 servings
Overhead view of butternut squash mac and cheese in bowl with fork
Prep: 40 minutes
Cook: 10 minutes
Total: 50 minutes

Ingredients
  

  • 1 pound roasted butternut squash 450 g
  • ½ pound pasta (gluten free if needed) 250g
  • 2 tablespoons olive oil divided
  • 2 chopped cloves of garlic
  • 1 medium shallot minced
  • 1 ½ cup whole milk
  • 5 ounces grated cheddar cheese 150 g
  • 4 ounces grated parmesan cheese, divided 120 g
  • 1 teaspoon garlic powder
  • 1 teaspoon onion Powder
  • Salt and pepper to taste

Instructions
 

  • Wash the squash, cut it in half, scoop out the seeds with a spoon. Brush with a spoonful of olive oil and bake in the oven at 350ºF for 30-40 minutes, until fork-tender. They should be nice and light golden brown when done.
  • Let it cool slightly, then scoop from the skin. You will need 1 pound of baked squash for the sauce, the rest could be frozen for later.
  • Cook your favorite pasta according to the package instructions.
  • While the pasta is cooking, heat 1 tablespoon of olive oil in a small saucepan, add chopped garlic and minced shallot. Sauté on medium heat for 1 minute, until fragrant.
  • Add 1 cup of milk, grated cheddar, half of the Parmesan, baked squash, spices and salt. Blend with an immersion blender until the mixture is smooth and consistent.
  • If you do not have an immersion blender, heat milk with the oil and garlic and pour it into the blender bowl, adding cheese and squash, spices and salt.
  • Return the butternut squash mixture back to the sauté pan over medium-high heat for 1 minute, stirring.
  • Taste and season the sauce with salt and pepper as needed (about 1/2 teaspoon salt and 1/4 teaspoon black pepper).
  • Mix the finished sauce with pasta and serve with more grated parmesan on top.
  • Optionally garnish with basil.

Notes

For a vegan option use:
  • 1 pound (450 g) roasted butternut squash
  • 1/2 pound (250g) pasta (gluten free if needed)
  • 2 tablespoons olive oil (divided)
  • 2 chopped cloves of garlic
  • 1 medium shallot, minced
  • 1 1/2 cup unsweetened plant milk (almond or soy works better)
  • 5 ounces (150 g) vegan cheddar cheese, grated
  • 2 tbsp nutritional yeast (or 4 ounces vegan parmesan)
  • 1 teaspoon garlic powder
  • 1 teaspoon onion powder
  • Salt and pepper to taste

Nutrition

Calories: 645kcal | Carbohydrates: 64g | Protein: 30g | Fat: 30g | Saturated Fat: 14g | Polyunsaturated Fat: 2g | Monounsaturated Fat: 11g | Cholesterol: 66mg | Sodium: 731mg | Potassium: 757mg | Fiber: 4g | Sugar: 9g | Vitamin A: 12779IU | Vitamin C: 25mg | Calcium: 773mg | Iron: 2mg
cuisine: American
course: Dinner, Side Dish

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