Butternut Squash Mac and Cheese

Creamy and delicious, this Butternut Squash Mac and Cheese is healthy comfort food that even picky eaters will love. With the sweet and savory flavors of fall, this recipe is great for cozy nights curled up on the couch. Also, it is pretty enough for holiday dinners.

This Butternut Squash Mac and Cheese is wonderful served alongside a Thanksgiving Turkey in addittion to extra creamy Red Skin Mashed Potatoes and a Festive Orange Spinach Salad. Also, I adore this pasta as a romantic dinner with the Best Rib Eye Steaks and my Arugula Pear Salad

A serving of Butternut Mac and Cheese on a brown plate.

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Overhead photo of Healthy Mac and Cheese garnished with red pepper flakes.

Healthy Comfort Food or Holiday Side Dish?

This Butternut Squash Mac and Cheese recipe actually is both. The butternut squash takes the place of the butter and milk that traditional Mac and Cheese has, thereby lowering the calories and really pumping up the nutrition. Don’t let all that healthiness fool you because it is creamy, savory and all around delicious. So delicious in fact that it makes a beautiful addittion to Thanksgiving and Christmas dinner. 

Tools Needed

  • Good Quality Knife– Butternut squash is fairly easy to cut as long as you have the right equipment. The most import tool for cutting this squash is a good quality chefs knife or Santoku knife. Both of these knifes you will find in the Chicago Cutlery set linked to at the beginning of this section. I adore Chicago Cutlery because they create affordable and quality knifes that last forever. I am still using my original knifes purchased through them back in the early 90’s. 
  • Cutting Board– Having a cutting board that doesn’t slip and slide is imperative to cutting butternut squash.
  • Vegetable Peeler– Butternut squash can be peeled using a knife but it is a thousand times easier using a comfortable vegetable peeler. 
  • Stockpots– To make this Butternut Squash Mac and Cheese you will need 2 stockpots, one for cooking the squash and one for boiling the pasta. (I adore my stainless steel pan set with glass lids. Also, I use my enameled cast iron Dutch Oven for cooking the squash.)
  • Blender– For the smoothest butternut squash sauce use a high speed blender to process the sauce. However, an immersion blender makes processing the sauce much easier but the sauce will not turn out as smooth in consistency. Note: A potato masher may also be used to process butternut squash. However, the sauce will be very chunky. 

How to Cut Butternut Squash

Steps showing how to cut butternut squash.

  1. Using a chefs knife carefully cut both ends off of the butternut squash.
  2. Cut the squash in half at the point where it curves. 
  3. Using a comfortable vegetable peeler peel the skin.
  4. Cut in half again.
  5. With a soup spoon remove the seeds.
  6. Place the pieces of squash with the cut side facing down and cut into strips.
  7. Cut the strips into cubes. 

Ingredients Needed

Butternut Squash Mac and Cheese ingredients on a white countertop.

  • Pasta (1 pound)- For this recipe tubular pasta or Conchiglie (shell pasta) works very well. 
  • Butternut Squash (1 medium or 2 pounds cubed)- Other winter squash such as acorn or kabocha squash may be used also. 
  • Brown Onion (aka, yellow onion)- About 1 1/2 cups diced.
  • Olive Oil– I believe passionately that a good quality olive oil makes a huge difference in home cooked meals. Look for olive oils that have an estate or mill name on the bottle along with a harvest date because real olive oil has a short life span.
  • Garlic– Chopping the garlic will impart great flavor into the broth and the remaining bits will be blended into the butternut squash sauce.
  • Bay Leaf– 1 dried bay leaf adds subtle sweet and savory flavors to the broth and squash. 
  • Chicken Stock (1 quart)- Or vegetable broth may be used.
  • Whole Milk– Low or nonfat milk may be used in addittion to flax or almond milk. However, whole milk will add a lovely creaminess. 
  • Salt– I started using Maldon’s Sea Salt Flakes for its low iodine content. Now I cook and bake with it all the time because it tastes amazing.
  • Black Pepper
  • Thyme– Compliments the bay leaf, sage and butternut squash.
  • Sage– This popular Thanksgiving herb is often described as being earthy or woody. However, it compliments the sweetness of the butternut squash beautifully. (Either rubbed or ground sage is perfectly fine for this recipe.)
  • Nutmeg– Very similar to the other herbs, nutmeg add a woody flavor that is a tasty contrast to the sweetness of the butternut squash. 
  • Cayenne Pepper– Adds a peppery spice that contrasts the sweetness of the butternut squash. (See “Making Kid Friendly Butternut Squash Mac and Cheese” section below for less spicy options.)
  • Parmigiano-Reggiano– This aged Italian cheese add a complex sharp flavor to this pasta dish. If Parmigiano-Reggiano is not available use the best quality parmesan cheese you can find. 
  • Sharp Cheddar Cheese– Or an aged cheese that brings in a ton of flavor such as Kerrygold. Note: Using shredded cheese from the grocery store is not recommended due to the anti-caking agents. Shredding your own cheese helps to create the creamiest results. 

Cheese Options

Butternut Squash, with its sweet nutty flavor, pairs well with cheese that has a more robust flavor and the meltability of the cheese is less of a concern. Choosing two of the options below will make this pasta very tasty. 

  • Sharp Cheddar Cheese
  • Sharp Cheddar Cheese
  • Gouda Cheese
  • Gruyère Cheese
  • Parmigiano-Reggiano
  • Fontina Cheese

Step by Step Instructions

Steps showing how to make Butternut Squash Mac and Cheese.

  1. In a large pot sauté onions in olive oil over medium-high heat until lightly translucent, about 8 minutes.
  2. Add garlic and sauté an additional minute.
  3. To the onions and garlic add the bay leaf, butternut squash and broth.
  4. Bring to a boil over high-heat. Once boiling lower to medium-low heat, cover and cook until squash is fork tender, about 20 minutes.
  5. Drain the squash into a colander placed over a bowl to reserve the broth. Remove bay leaf.
  6. Transfer cooked squash back into original pot and add milk. 
  7. To the squash add salt, pepper, thyme, nutmeg, cayenne pepper and sage. Bring to a simmer over medium heat for 2-3 minutes.
  8. Transfer butternut squash mixture to a blender and process squash until smooth. Add in just enough of the reserved broth to loosen the consistency to a thick soup. Note: For easier processing use an immersion blender. However, the sauce will not be as smooth. 
  9. Add butternut squash puree back into original pot.
  10. Sprinkle in cheese.
  11. Stir well until cheese melts.
  12. Add in al dente pasta and stir well. 

Note: Put the water on to boil at least halfway through cooking the squash. Cook pasta according to package instructions and start just before processing the sauce in the blender. 

Squash Mac and Cheese serve on a small dinner plate that is sitting on a wooden table.

Making Kid Friendly Butternut Squash Mac and Cheese

This Butternut Squash Mac and Cheese is such a great way to get kids to eat more veggies because the creamy sauce is a wonderful disguise. However, to make it even more kid friendly you will definitely want to change up the seasoning a bit.

Instead of using cayenne pepper, replace it with 1 teaspoon of smoked paprika. Also, some kiddos my not enjoy sage so it may be best to leave it out.

Additionally, softer cheese such as mozzarella, havarti or provolone may be a good substitution for the sharp cheddar and make it even more tasty for kiddos. 

Frequently Asked Questions

Would this recipe work well with another type of squash?

Absolutely! Any one of the winter squashes will work. However, the texture may vary from one squash to another. 

Can bacon be added?

This pasta would taste amazing with bacon. To add bacon cut 3-4 pieces into strips and fry in a pot over medium heat until crisp. Remove bacon pieces with a slotted spoon and place onto a paper towel lined plate. Remove all by 2 tablespoons of the bacon fat from the pot and use the remaining fat to sauté the onions. Follow the directions as written but add the bacon pieces back into the butternut squash puree before adding the cooked pasta.  

How long will this last in the refrigerator? 

Believe it or not, this pasta tastes even better the second day. Store leftovers in the refrigerator in an airtight container for up to 4 days. Reheat individual portions in the microwave uncovered for 3 minutes on power level 8. 

Can Butternut Squash Mac and Cheese be frozen?

Yes, I currently have some divided into individual freezer containers in my freezer at this moment that is perfect for heating up on busy weeknights.

For the best results, defrost in the refrigerator over night and the heat on power level 8. It could take approximately 8-10 minutes to heat but it is best to start with 3 minutes, stir and add on smaller amounts of time until it heated to a desired temperature. 

More Healthy Comfort Recipes You Will Love

Creamy Butternut Tortellini Soup

Sweet Potato Cakes

Oat Flour Pancakes

Chocolate Yogurt Parfait

Sticky Lemon Chicken

Egg Roll in a Bowl  

Up close photo of Butternut Mac and Cheese.

Butternut Squash Mac and Cheese

This Butternut Squash Mac and Cheese is the ultimate healthy cozy comfort food that is also perfect for Holiday meals. The butternut squash takes the place of the traditional béchamel sauce but is no less luxurious.
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Course: Dinner, Side Dish
Cuisine: American
Keyword: Butternut Squash Mac and Cheese, Healthy Mac and Cheese
Prep Time: 15 minutes
Cook Time: 25 minutes
Servings: 10 servings
Calories: 368kcal
Author: Heather

Ingredients

  • 1 medium butternut squash *peeled, deseeded and cubed See Note #1 below
  • 1 medium brown onion (aka yellow onion) *diced, about 1 1/2 cups
  • 2 tablespoons olive oil
  • 4 large garlic cloves *chopped
  • 1 bay leaf See Note #2 below
  • 4 cups chicken broth *or vegetable broth
  • 1 1/4 cups whole milk See Note #3 below
  • 1 teaspoon salt
  • 1/4 teaspoon pepper
  • 1 teaspoon thyme
  • 1/2 teaspoon nutmeg
  • 1/2 teaspoon cayenne pepper *see "Making Kid Friendly Butternut Squash Mac and Cheese" section above for less spicy alternatives.
  • 1/2 teaspoon sage
  • 1/2 cup freshly grated parmesan
  • 2 cups sharp cheddar
  • 1 pound pasta

Instructions

Cooking Squash

  • In a large pot sauté onions in olive oil over medium high heat until lightly translucent, about 8 minutes. Add garlic and sauté an additional minute.
  • To the onions and garlic add the bay leaf, butternut squash and broth. Bring to a boil over high heat. Once boiling lower heat to medium low, cover and cook until squash is fork tender, about 20 minutes.
  • Drain the squash into a colander placed over a bowl to reserve the broth. Remove bay leaf.

Butternut Mac and Cheese

  • About halfway through cooking the squash place a large pot of water on to boil. Once boiling, cook the pasta to al dente following the directions on the package.
  • Transfer cooked squash back into original pot. To the squash add milk, salt, pepper, thyme, nutmeg, cayenne pepper and sage. Bring to a simmer over medium heat for 2-3 minutes.
  • Using an immersion blender (See Note #4 below), process squash until smooth. Add in just enough of the reserved broth to loosen the consistency to a thick soup.
  • Turn off the heat and add cheese. Stir well.
  • Add cooked pasta and stir well.

Notes

Recipe Notes
Note #1- Once the butternut squash is peeled, deseeded and cubed it will be about 2 pounds. 
Note #2- Use 2 bay leaves if small. 
Note #3- Low-fat, nonfat and dairy free milks may be substituted but will not be as creamy as whole milk. 
Note #4- For an extra smooth sauce transfer to a high speed blender rather than using an immersion blender. 

Nutrition

Calories: 368kcal | Carbohydrates: 47g | Protein: 16g | Fat: 14g | Saturated Fat: 7g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 5g | Cholesterol: 30mg | Sodium: 817mg | Potassium: 533mg | Fiber: 3g | Sugar: 5g | Vitamin A: 8342IU | Vitamin C: 24mg | Calcium: 315mg | Iron: 2mg
Tried this recipe?Mention @thefedupfoodie or tag #thefedupfoodie!

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