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Butternut Squash Mac and Cheese

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Butternut Squash Mac and Cheese is comfort food with a seasonal twist. Creamy, cheesy and ultra-satisfying, it features butternut squash blended into a silky cheese sauce for a subtle sweetness and an extra layer of flavor. It's the perfect cozy dish for fall and a unique spin on classic mac and cheese!

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.

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.

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!

It's a cozy, kid-friendly twist on a comfort food favorite!

🥘 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 (scroll down for the details). This is an easy recipe with shortcuts!

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

Nutmeg: Nutmeg adds a distinctive and subtle nuttiness.

Pasta: Use a small, bite-sized pasta. My favorite is (affiliate link) mezzi rigatoni.

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

⭐ Pro Tip

For a tip on a highly recommended brand of cheddar cheese, check out this article where I was among the experts quoted. Spoiler Alert: It's Tillamook Medium Cheddar, a favorite brand from the Northwest!

Diced butternut squash on a marble counter.

📋 How to Prep the Butternut Squash

Here are four great options to prepare the butternut squash for mac and cheese. Scroll down to choose your option depending on how much time you have.

My favorite is option is #3.

Option 1: Oven Roast the Squash

Baked butternut squash, mashed lightly.

How Long It Takes: The cooking time to oven-roast a whole butternut squash is about 90 minutes.

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 the Squash

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 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.

Prep: 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.

Cook: 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 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

Here's how to make Butternut Squash Mac and Cheese. It's a pretty simple recipe.

Cook ½ pound of pasta in about 2 quarts of water in a medium-sized pot on the stove. Cook the pasta for 9 minutes and drain in a colander or strainer. Set aside.

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

Three types of grated cheese mounded on a cutting board.

Reserve ¼ cup each of smoked Gouda, Parmesan and Cheddar cheeses.

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

Blend the cheese sauce ingredients in the same pot used to boil the pasta. Remove the pan from the stove and stir in the 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.

Large dish of mac and cheese with a serving spoon scooping up a portion.

Place the pasta mixture in a pan and cover with foil. Bake for 20 minutes.

Top the pasta with the reserved cheese and return it to the oven. Continue baking uncovered for an additional 10-20 minutes.

⭐ Pro-Tip

If you use a baking dish larger than two quarts, reduce the cooking time by about 10 minutes since the ingredients will be spread out in the larger dish.

🍽 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!

Note: The Crinkled Cookbook is not in any way affiliated with Trader Joe's.

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.

Do I need to peel butternut squash before roasting it?

Leave the peel on. Regardless of which baking technique you use, the cooked squash is easy to scoop out after baking and cooling.

Can I freeze this?

Yes. Just like Trader Joe's does! 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/

🍲 Storing Leftovers

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.

🍴More Comfort Food Recipes

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. I look forward to hearing from you!

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 475 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 

  • ⅔ cup cooked, mashed butternut squash - about 1 pound of squash before cooking or 3 cups diced squash
  • 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
  • ¼ cup butter - unsalted
  • ¼ cup flour
  • 2 cups milk
  • 1 teaspoon salt
  • ½ teaspoon nutmeg - ground
  • ⅛ teaspoon ground pepper
  • ¼ teaspoon tabasco sauce

Instructions

Prep the Squash and Cook the Pasta

  • Scroll down to METHODS FOR PREPARING BUTTERNUT SQUASH and select the option that works best for you to cook and mash the squash.
    Preheat oven to 350° and spray a 2-quart baking dish with Pam or grease with shortening.
  • 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.
    Reserve ¼ cup of each cheese to use as a topping after the first baking stage.
    ½ pound mezzi rigatoni, 1 ¼ cup cheddar cheese, ¾ cup smoked gouda cheese, ½ cup parmesan cheese
  • Drain the pasta in a colander and leave the pasta there while you make the sauce.

Prepare the Cheese Sauce

  • Use the same pan used to cook the pasta, melt the butter and whisk in the 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 a thick cream sauce.
    ¼ cup butter, ¼ cup flour, 2 cups milk
  • Remove from the heat and stir in the cheddar, smoked gouda and parmesan cheeses along with the cooked and mashed butternut squash.
    Add the nutmeg, tabasco, salt and pepper and stir.
    Add the pasta and stir again.
    1 teaspoon salt, ½ teaspoon nutmeg, ⅛ teaspoon ground pepper, ¼ teaspoon tabasco sauce

Bake

  • Place the cheese, squash and pasta mixture into the prepared baking dish.
  • Cover the dish with foil and bake for 20 minutes. Remove from the oven, remove the foil and sprinkle the reserved cheese on top. Return the pan to the oven and bake uncovered for an additional 15 minutes or until hot and bubbly around the edges.
  • Let the dish sit for a few minutes before serving. As an option, garnish with a dash of paprika and parsley. Serve and enjoy!

METHODS FOR PREPARING BUTTERNUT 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 it with foil and let it 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 can be mashed easily.
    Canned butternut squash is perhaps the easiest alternative. Simply open the can and the squash is pureed and ready to use.
    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.
    ⅔ cup cooked, mashed butternut squash

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

Nutrition

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. The data above is 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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    4.96 from 475 votes (451 ratings without comment)

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  1. Karen says

    5 stars
    I didn't have tabasco on hand and used sriracha in it's place. Recipe Perfection. Will serve as a side for this coming Thanksgiving. Yum.

    Reply

    • Melinda O'Malley Keckler says

      Hi Karen, Good thinking with the hot sauce substitution. Thank you for the five star rating! I'm glad you enjoyed this new spin on mac and cheese. 🙂

      Reply

  2. megane says

    5 stars
    the only way to have mac and cheese. Smoky pumpkin-y goodness!

    Reply

    • Melinda O'Malley Keckler says

      Thank you Megan. I'm glad to hear you enjoyed it!

      Reply

  3. Julie says

    5 stars
    I made this recipe for my daughter returning from Uni for a few days and she loved it, especially the three different cheeses. Mac and cheese has always been her favourite and your version with squash hit the spot. thanks!

    Reply

    • Melinda O'Malley Keckler says

      I'm glad to hear your daughter enjoyed it Julie! Thanks for the five star review. 🙂

      Reply

    • Melinda O'Malley Keckler says

      Hi Julie, I'm thrilled to hear you loved this recipe!! It truly is a decadent spin on homemade mac and cheese. My kids love it too.

      Reply

  4. Freya says

    5 stars
    The sweetness of the squash with the Smokey cheese: this was just wow!!

    Reply

  5. nancy says

    5 stars
    there's mac and cheese and then there's butternut squash mac and cheese!

    Reply

  6. Andrea says

    5 stars
    love this butternut squash version of mac n cheese! so so good!

    Reply

  7. Jere Cassidy says

    5 stars
    After making this mac and cheese recipe I may never go back to the regular one. The squash was a little extra work, but so worth it. The flavor with all these cheeses is amazing.

    Reply

    • Melinda O'Malley Keckler says

      I'm so glad to hear you loved it Jere! A good shortcut with the butternut squash is to buy it pre-cubed or even frozen. Thanks for the five stars!!

      Reply

  8. Julia says

    Yum, this was so creamy and I'm always a fan of adding some butternut squash to recipes when I can. Reminds me of the ones I use to get at TJ's but so glad I'm making this at home now instead.

    Reply

  9. Oscar says

    5 stars
    The butternut squash with the smoked gouda made this mac and cheese over-the-top delicious. It was super creamy and surprisingly easy to make. Thanks for the recipe.

    Reply

  10. nancy says

    5 stars
    this mac and cheese with butternut squash is so wonderful and creamy.

    Reply

  11. Leah says

    I want to make this, but want to confirm that the pasta goes into the dish uncooked. Is there enough liquid for the pasta to fully hydrate?

    Reply

    • Melinda O'Malley Keckler says

      Hello! Please DO cook the pasta first. 🙂

      Reply

    • Daisy Songbird says

      You need to read the recipe. It tells you to cook the pasta!

      Reply

  12. Mama Maggie's Kitchen says

    5 stars
    I bet this is as good as it looks. YUMMMM!

    Reply

  13. Chef Dennis says

    5 stars
    This is making me hungry!

    Reply

  14. Kayla DiMaggio says

    5 stars
    Yum! I love butternut squash and the smoked gouda cheese in the dish was so delicious!

    Reply

  15. Jeannie says

    5 stars
    Fall is just around the corner but never too early to enjoy this recipe! It looks so good, I need to find butternut squash now.

    Reply