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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 squash, cheese and pasta. The butternut squash cheese sauce is silky and creamy and includes seasonings that are light and just a bit nutty. It's an impressive meatless main dish or a rich side dish with natural sweetness and the velvety texture of butternut squash. Serve it with crisp salad greens and Blue Cheese Vinaigrette along with Four Ingredient Basic Biscuits for a cheesy, 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

Like every recipe from the Crinkled Cookbook, Butternut Squash Mac and Cheese is tried and true, and wow is it delicious.

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!

Much like No Ketchup Meatloaf or Chicken Spaghetti with Rotel and Velveeta, it's classic comfort food. I've served this recipe countless times and it's always a winner.

From a weeknight main dish to a holiday side, Butternut Squash Mac and Cheese contributes to a delicious meal!

🥘 Ingredients to Have on Hand

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

Butternut Squash: There are several options for creating creamy, baked butternut squash so be assured, you won't necessarily need to roast an entire squash. This is an easy recipe to make and there are shortcuts!

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

Nutmeg: The ultimate spice to add to creamy, cheesy recipes. 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. Any pasta you would use for traditional mac and cheese will work well with butternut squash mac and cheese.

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 very distinctive flavor, but if you're looking for substitutions you'll want to use vegetables that have a very similar texture and flavor. Here are a few I recommend:

Acorn Squash: This is a close cousin to butternut squash and it also has a slightly nutty flavor.

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. It has a slightly milder flavor but is still quite delicious.

📋 How to Prepare the Butternut Squash for Mac and Cheese

There are four great options to prepare butternut squash for mac and cheese. None are hard, but several will take a few more minutes than the others.

Choose your option depending on how much time you have.

Scroll down for the four options.

Option 1: Oven Roast Butternut Squash

Baked butternut squash, mashed lightly.

Time Tip: 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. A few lumps are fine.

Option 2: Microwave Butternut Squash

Time Tip: 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.

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 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.

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.

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.

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 Butternut Squash

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

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

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.

This is my favorite shortcut to buy butternut squash from the grocery store peeled, sliced and diced.

Option 4: Buy Frozen or Canned Butternut Squash

Time Tip: Canned butternut squash is perhaps the easiest option. Open the can and the squash is pureed and ready to use in mere seconds!

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

🥘 Make Butternut Squash Mac and Cheese Step-By-Step

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.

The butternut squash cheese sauce begins with what my Mom would call a good old-fashioned white sauce.

But since the sauce is seasoned with nutmeg, it becomes what very fancy folks in the kitchen might call a classic béchamel sauce. I like how Bon Appetite magazine explains what that pretty name actually means.

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, and especially after seeing how much my daughter enjoyed that version of the classic fall dish.

Trader Joe's Butternut Squash Mac and Cheese has a bit more of a sage flavor than my recipe, but I think you'll agree, there is a strong similarity.

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. Those offer a similar creaminess and sweetness to mac and cheese but keep in mind the flavors will be distinctively different.

🍲 Storing Leftovers and Freezer Tips

Store Butternut Squash Mac and Cheese leftovers in a covered 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 comfy 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. Serve with Four Ingredient Basic Biscuits for classic comfort food!
4.94 from 365 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. 

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 and are offered here only as a guideline for informational purposes.

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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