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Butternut Squash Mac and Cheese

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Butternut Squash Mac and Cheese is a creamy and satisfying combination of cheese and pasta. The butternut squash cheese sauce is silky smooth and includes light seasonings with a hint of nuttiness. It's an impressive meatless main dish or a rich side dish with the natural sweetness of butternut squash.

Serve this unique spin on mac and cheese with crisp salad greens topped with Blue Cheese Vinaigrette or Pan-Roasted Asparagus and Four Ingredient Basic Biscuits for a delicious meal!

Large dish of mac and cheese with a serving spoon scooping up a portion.
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👩🏻‍🍳Why You'll Love Butternut Squash Mac and Cheese

Much like No Ketchup Meatloaf or Chicken Spaghetti with Rotel and Velveeta, Butternut Squash Mac and Cheese is classic comfort food. I've served this mac and cheese countless times and everyone always asks for the recipe!

It's a copycat recipe inspired by Trader Joe's delicious Butternut Squash Mac and Cheese. But rather than being limited to a single serving, make an entire batch and enjoy!

🥘 Ingredients to Have on Hand

Butternut Squash Mac and Cheese ingredients in small dishes with labels.

Butternut Squash: There are several ways to prepare butternut squash for this recipe so be assured (scroll down for the details) this is an easy recipe to make and there are shortcuts!

Cheddar, Smoked Gouda and Parmesan Cheese: Together three cheeses add amazing, rich cheesy flavor to the silky butternut squash.

Nutmeg: Nutmeg adds a distinctive and very subtle nutty flavor.

Pasta: Use a small, bite-sized pasta. You'll want a pasta shape that will hold the creamy sauce. My favorite is (affiliate link) mezzi rigatoni.

Scroll down for step-by-step instructions and specifics on the quantities for each ingredient.

Diced butternut squash on a marble counter.

📖 Substitutions

Butternut squash has a distinctive flavor, but if you're looking for substitutions here are a few I recommend:

Acorn Squash: Flavor-wise, this is a close "cousin" to butternut squash.

Sweet Potatoes: Baked and peeled sweet potatoes have a sweet and slightly nutty flavor and their texture is similar to butternut squash when roasted or mashed.

Pumpkin: Pureed pumpkin, especially sugar pumpkin or pie pumpkin can be used in place of butternut squash.

📋 How to Prep Butternut Squash

Here are four great options, with step-by-step instructions to prepare butternut squash for mac and cheese. Choose your option depending on how much time you have.

Option 1: Oven Roast

Baked butternut squash, mashed lightly.

How Long It Takes: The cooking time to oven-roast a whole butternut squash is about 90 minutes, depending on the size of the squash.

Cut the Squash in Half: If you're using a whole squash, carefully cut it in half lengthwise and scoop out the seeds. Leave the peel on and place the squash peel side down in a glass baking dish.

Bake: Pour about ½ cup of water into the dish to help keep the squash moist while it cooks. Bake uncovered at 350° F for about 90 minutes.

Cool and Mash: Once the squash is soft and tender, remove it from the oven, cover with foil and let it cool slightly so it will be easier to handle. Once cooled, use a sturdy spoon to scoop out the cooked squash. Use a potato masher or a fork to create a semi-smooth consistency.

Option 2: Microwave

How Long it Takes: The cooking time to microwave a butternut squash is about 30 minutes, depending on the size of the squash and the wattage of your microwave.

A knife slicing the end off of a butternut squash.
A fork making small holes in the peel of an uncooked butternut squash. The ends are sliced off and by the side as is a knife.

Remove the Ends: Slice the ends off of the butternut squash and pierce the peel about a dozen times with a fork.

A butternut squash after cooking it in the microwave. The peel is dimpled and the squash is tender.
Two halves of butternut squash, cooked, on a cutting board with a small bowl on the side.

Cook: Place the whole squash in the microwave oven on high for 20 minutes. Check to see if the squash is tender. If not, continue cooking and checking it at 10-minute intervals.

A spoon is scooping out the cooked butternut squash from the peel and into a bowl.
A potato masher being used to mash cooked butternut squash in a medium-sized bowl.

Cool and Mash: Once the squash is soft, remove it from the microwave, cover it with foil and let it rest for 15 minutes. Slice the cooked squash in half lengthwise. Scoop out the seeds and discard. Use a spoon to scoop out the cooked butternut squash. Place it in a medium-sized bowl and use a potato masher to create a smooth consistency.

Option 3: Buy Pre-Cubed Squash

Diced butternut squash spread out in a glass baking dish on a placemat.

How Long It Takes: The cooking time to microwave pre-sliced and cubed butternut squash is about 15 minutes, depending on the wattage of your microwave.

Cook: If you've purchased the butternut squash (affiliate link) pre-sliced and cubed from the grocery store, place the squash cubes in a shallow pan, cover with parchment paper or waxed paper and add a tablespoon of water.

Mash: Depending on your microwave, it should take about 15 minutes on high power. Check the squash at 15 minutes, it should be very tender and mash easily with a fork.

Option 4: Buy Frozen or Canned Butternut Squash

How Long It Takes: (Affiliate link) Canned butternut squash is perhaps the easiest option. Open the can and the squash is pureed and ready to use in mere seconds!

If (affiliate link) frozen, cook the butternut squash according to the package directions or until it's fork-tender and will mash easily.

🥘 Step-By-Step Instructions

Cook ½ pound of pasta in about 2 quarts of water in a medium-sized pot on the stove.

I recommend using bite-sized pasta for this recipe.

My favorite size and shape is mezzi rigatoni, which is a rigatoni that's slightly smaller than standard rigatoni pasta.

Other good options include elbow macaroni, penne pasta or shells.

Cook the pasta for 9 minutes and drain in a colander or strainer. Set aside.

Shredded cheeses, butternut squash spices and cream sauce in a pan with a wise.

Use the same pot you cooked the pasta in, to create the creamy, cheesy butternut squash sauce.

Melt ¼ cup of butter in the pan over medium-high heat and whisk in ¼ cup of flour.

Stir over medium heat until the butter is foamy, and then whisk for about 20 seconds.

Add two cups of milk and continue stirring until the milk becomes a thick cream sauce.

Three types of grated cheese mounded on a cutting board.

Reserve ¼ cup each of smoked gouda and cheddar cheeses.

Remove the pan from the stove and stir in the grated cheddar, smoked gouda and parmesan cheeses along with the cooked butternut squash.

Add nutmeg, Tabasco sauce, salt and pepper and stir.

Pasta and cheese sauce in the pan, being stirred with a wooden spoon.

Add the cooked pasta to the cheesy sauce in the pan and stir to combine.

Spray a 2-quart glass baking dish with Pam, or grease with shortening.

Preheat oven to 350° F.

Place the pasta combined with butternut squash cheese sauce into the pan and cover with foil. Bake for 20 minutes. Remove the dish from the oven.

Top the pasta with the reserved gouda and cheddar cheese and return to the oven. Continue baking uncovered for an additional 10-20 minutes or until hot and bubbling.

Pro-Tip

If you use a dish larger than two quarts, reduce the cooking time by about 10 minutes.

Mac and cheese in a dish with a serving spoon.

🍽 Inspired by Trader Joe's Butternut Squash Mac and Cheese

I was inspired to come up with this recipe after tasting Trader Joe's Butternut Squash Mac and Cheese. Trader Joe's version has a stronger sage flavor than my recipe, but I think you'll agree, they are close!

The best part about making Butternut Squash Mac and Cheese at home is you have much more to enjoy than what we get from just one frozen package.

Note: The Crinkled Cookbook is not in any way affiliated with Trader Joe's. This recipe was simply inspired by their delicious Butternut Squash Mac and Cheese, which is sold in their frozen foods section.

A baking dish of butternut squash mac anc cheese with a large serving spoon.

💭 Recipe FAQs

Can I use canned or frozen butternut squash?

Yes! Either frozen or canned butternut squash will work great. But I think the texture and flavor are far better in the butternut cheese sauce when we use fresh, oven-roasted squash in this recipe.

Do I need to peel butternut squash before roasting it?

Leave the peel on. Regardless of which baking technique you use - oven roasting or microwaving - the cooked squash is easy to scoop out of the peel after the squash bakes.

Can I use a different type of squash?

I believe butternut squash is best to use in this recipe. But acorn squash, sweet potatoes or even pumpkin are good alternatives.

🍲 Storing Leftovers and Freezer Tips

Store Butternut Squash Mac and Cheese leftovers in a covered, airtight container in the refrigerator and plan to enjoy them within 3-4 days.

The cheese sauce tends to tighten up a bit when it's chilled, so you may want to sprinkle a few drops of water on the top before reheating. This will help soften the sauce as it warms up.

Butternut Squash Mac and Cheese is best served the day you make it, but it does freeze well. After baking and cooling, cover the dish tightly with aluminum foil and freeze for up to 3 months.

To reheat, remove the dish from the freezer and place it in the refrigerator to defrost for 24 hours.

After defrosting, place the covered baking dish in a 350° F oven and reheat the mac and cheese for 30 - 45 minutes or until bubbly and hot.

Note: The pasta may be less al dente than when it was fresh from the oven. Also, the cheese sauce may need a few drops of water added to the top as you reheat it to help it return to its original silky texture.

🍴More Recipe Ideas

Butternut Squash Mac and Cheese is a classic comfort food and a delicious main dish. Here are a few more of my favorite recipes, including dessert, that also fit that comfort food description.

If you tried Butternut Squash Mac and Cheese or any other recipe on my website, please leave a 🌟 star rating and let me know how it goes in the 📝 comments below.

Recipe

Mac and cheese in a dish with a serving spoon.

Butternut Squash Mac and Cheese

A silky, savory and satisfying combination of butternut squash, three cheeses and pasta. This is a wonderful meatless main dish or an impressive side. And here's another new spin on mac and cheese - Smoked Gouda Mac and Cheese. Serve with Four Ingredient Basic Biscuits for classic comfort food! And follow dinner with one of these 15 Best Dessert Recipes with Apple and Pumpkin.
4.96 from 473 votes
Print Rate Pin Recipe
Prep Time: 40 minutes
Cook Time: 30 minutes
Total Time: 1 hour 10 minutes
Servings: 6
Calories: 461kcal
Author: Melinda O'Malley Keckler

Ingredients 

  • 3 cups diced butternut squash - about 1 pound of squash, you’ll need ⅔ cup of cooked, mashed squash
  • 2 cups milk
  • ¼ cup butter - unsalted
  • ¼ cup flour
  • ½ pound mezzi rigatoni - or any small shaped pasta such as elbow macaroni or penne
  • 1 ¼ cup cheddar cheese - shredded
  • ¾ cup smoked gouda cheese - shredded
  • ½ cup parmesan cheese - shredded
  • ½ teaspoon nutmeg - ground
  • ¼ teaspoon tabasco sauce
  • 1 teaspoon salt
  • ⅛ teaspoon ground pepper

Instructions

  • Preheat oven to 350° and spray a 2-quart baking dish with Pam or grease with shortening.

Select Method for Cooking the Squash

  • Oven-Roast Butternut Squash:
    If you're using a whole squash, carefully cut it in half lengthwise and scoop out the seeds. Leave the peel on and place the squash peel side down in a glass baking dish.
    Pour about ½ cup of water into the dish to help keep the squash moist while it cooks. Bake uncovered at 350° F for about 90 minutes. The cooking time will vary based on the size of the squash. Once the squash is soft and tender, remove it from the oven, cover with foil and cool slightly so it will be easier to handle. Scoop the cooked squash out of the peel.
    Microwave Butternut Squash:
    Slice the ends off of the butternut squash and pierce the peel about a dozen times with a fork.
    Cook in the microwave oven on high for 20 minutes. Check to see if the squash is tender. If not, continue cooking and checking it at 10-minute intervals. Once the squash is soft, cover it with foil and let it rest for 15 minutes. It may take slightly longer for the squash to be cool enough to handle. Slice the cooked squash in half, remove the seeds, and use a spoon to scoop out the cooked squash.
    Buy Frozen or Canned Butternut Squash:
    If frozen, cook the butternut squash according to the package directions or until it's fork-tender and will mash easily.
    Canned butternut squash is perhaps the easiest alternative. Simply open the can and the squash is pureed and ready to use.
    If you've purchased the butternut squash pre-sliced and cubed from the grocery store, place the squash cubes in a shallow pan, cover with parchment paper or waxed paper and add a tablespoon of water.
    Depending on your microwave, it should take about 15 minutes on high power. Check the squash at 15 minutes, it should be very tender and mash easily with a fork.
    Buy Butternut Squash Prepped and Cubed:
    If you've purchased the butternut squash pre-sliced and cubed from the grocery store, place the squash cubes in a shallow pan, cover it with parchment paper or waxed paper, and add a tablespoon of water. Depending on your microwave, it should take about 15 minutes on high power. Check the squash at 15 minutes, it should be very tender and mash easily with a fork.
    Mash the cooked squash - either oven roasted or microwaved - with a fork or potato masher to create ⅔ cup of cooked squash.
    Set it aside until the cheese sauce is ready.

Cook Pasta

  • Cook pasta on the stovetop using the minimum cooking time listed on the packaging. For mezzi rigatoni (small rigatoni) it’s about 9 minutes. While the pasta is cooking, shred all three of the cheeses.
    Set aside about ¼ cup of the Cheddar and ¼ cup of the Gouda, that will be used for the topping.
  • Drain pasta in a colander and leave the pasta there while you make the sauce.

Prepare Cheese Sauce

  • Use the same pan used to cook the pasta, melt the butter and whisk in flour. Stir over medium heat until the butter is foamy, and whisk for about 20 seconds.
    Add two cups of milk and continue stirring until the milk becomes like a thick cream sauce.
  • Remove from heat and stir in the cheddar, smoked gouda and parmesan cheeses along with the cooked butternut squash.
    Add nutmeg, tabasco, salt and pepper and stir.
    Add macaroni and stir again.

Bake

  • Place ingredients into prepared baking dish.
  • Cover the dish with foil and bake for 20 minutes. Remove from oven, remove foil and sprinkle the reserved cheddar and gouda on top of the hot macaroni. Return to the oven and bake for an additional 15 minutes or until hot and bubbly around the edges.
  • As an option, garnish with a dash of paprika and a little parsley.

Notes

The cooking time for this recipe takes into account the time needed to cook pre-cubed butternut squash in the microwave. Oven roasting the squash will add at least 90 minutes to the recipe's time. Follow up Butternut Squash Mac and Cheese with a tasty, family-favorite dessert such as Old Fashioned Strawberry Rhubarb Pie or my Best Blueberry Cake Recipe
Calories: 461kcalCarbohydrates: 29gProtein: 22gFat: 29gSaturated Fat: 18gCholesterol: 93mgSodium: 953mgPotassium: 437mgFiber: 2gSugar: 7gVitamin A: 8277IUVitamin C: 15mgCalcium: 606mgIron: 2mg

Please note, the nutrition details are estimated using a food database, so they’re just a rough estimate not an exact science.

Did you try this recipe? Leave a comment below or @crinkledcookbook on Instagram, snap a photo and tag it #crinkledcookbook

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Comments

    4.96 from 473 votes (451 ratings without comment)

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  1. Sarah says

    I made this using canned pumpkin, almond milk and veggie ground round! Sooo delicious! Will definitely make again!

    Reply

    • Melinda O'Malley Keckler says

      Glad you enjoyed the recipe Sarah! Thanks for sharing your substitutions.

      Reply

  2. Melissa says

    5 stars
    Macaroni and cheese is mostly carbs and fat…adding the squash makes me feel better that we’re getting veggies too. I added a touch more hot sauce in mine because I like a little more heat. Plenty to share with my neighbors and they said it was crazy good!

    Reply

    • Melinda O'Malley Keckler says

      Thank you Melissa, I appreciate you leaving a comment and how nice that you shared with neighbors! 🙂

      Reply

  3. Amy says

    5 stars
    Really delicious recipe and love having vegetables in mac and cheese.

    Reply

    • Melinda O'Malley Keckler says

      Thanks Amy. I agree! Butternut squash is a delicious companion to mac and cheese!

      Reply

  4. Sonja says

    5 stars
    This might be my favourite Mac and Cheese recipe, as it has a healthy dose of veggies smuggled in and yet is super creamy. The slight sweetness of the sqaush makes it even better.

    Reply

    • Melinda O'Malley Keckler says

      Thank you for the five star rating Sonja!

      Reply

  5. Jacqueline. says

    5 stars
    I love the flavour of roasted butternut squash and it blended so well with the pasta and cheese sauce. Much more flavourful than a normal mac and cheese!

    Reply

    • Melinda O'Malley Keckler says

      Glad you enjoyed it. Butternut squash in mac and cheese is a game changer!

      Reply

  6. Oscar says

    5 stars
    Omgosh, this was super delicious. All that cheese with the butternut squash is so dreamy. love this mac and cheese recipe.

    Reply

    • Melinda O'Malley Keckler says

      Thanks Oscar!

      Reply

  7. Claudia says

    5 stars
    I tried making Butternut Squash Mac and Cheese, and it’s awesome! Creamy, cheesy, and the squash adds a nice twist. A perfect comfort food makeover!

    Reply

    • Melinda O'Malley Keckler says

      Thank you Claudia! I'm glad you enjoyed it.

      Reply

  8. Jill says

    5 stars
    Great recipe, thank you! The squash gives it a nice sweet, creamy texture & taste and adds moisture. Better than I thought it would be. A new favorite.

    Reply

    • Melinda O'Malley Keckler says

      Thank you Jill, it's a favorite in our house too!! Butternut squash is pure magic in mac and cheese. 🙂

      Reply

  9. Michelle says

    I'm confused, do we need 3 cups of butternut squash or just 2/3 cup?

    Reply

    • Melinda O'Malley Keckler says

      Hi Michelle, You'll need 2/3 cup of cooked, mashed butternut squash. If you have about 3 cups of cubed, or diced, uncooked butternut squash it will cook down and equal about 2/3 cup when mashed.

      Reply

  10. lindalee says

    5 stars
    This was delicious! I didn't measure my cheese so probably added more than was called for. Also, I had to add double the butter for the roux as it became one big glob with just the 2 tbsp and the flour. (Maybe I just don't know how to do it with the ratio provided) My husband and daughter were skeptical but loved it too. My daughter's 25, haha.

    Reply

    • Melinda O'Malley Keckler says

      Thank you for the five-star rating and I'm so happy your family enjoyed it! The recipe calls for 1/4 cup butter and 1/4 cup flour so you did the right thing by adding more after starting with 2 tablespoons of butter. I often add more cheese too!! 🙂

      Reply

  11. Stephanie says

    5 stars
    The whole family liked it and requested it be added to the regular rotation. I added a Ritz cracker topping with melted butter, paprika, garlic, salt and parmesan cheese. I also snuck in some nutritional yeast for vitamins. Thanks for a winner dish!

    Reply

  12. Katie says

    Can this be prepared a day ahead of time? Will it still taste just as good?

    Reply

    • Melinda O'Malley Keckler says

      Hi Katie, This can be prepared in advance, but the cheese sauce tends to tighten up a bit when it's chilled, so you may want to sprinkle a few drops of water on the top before reheating. This will help soften the sauce as it warms up.

      Reply