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Oct 18, 2020 · Modified: Jul 31, 2021 by Melinda O'Malley Keckler · This post may contain affiliate links · this blog generates income via ads.

Butternut Squash Mac and Cheese

Name: Butternut Squash Mac and Cheese
Prep time: 40 min
Cook time: 30 min
Total time: 70 min
Ingredients: 3 cups diced butternut squash (about 1 pound of squash, you’ll need 2/3 cup of cooked, mashed squash); 2 cups milk; 1/4 cup butter (unsalted); 1/4 cup flour; 1/2 pound mezzi rigatoni (or any small shaped pasta such as elbow macaroni or penne); 1 1/4 cup cheddar cheese (shredded); 3/4 cup smoked gouda cheese (shredded); 1/2 cup parmesan cheese (shredded); 1/2 teaspoon nutmeg (ground); 1/4 teaspoon tabasco sauce; 1 teaspoon salt; 1/8 teaspoon ground pepper

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Butternut Squash Mac and Cheese is a creamy and satisfying combination of squash, cheese and pasta. The butternut 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.

Large dish of mac and cheese with a serving spoon scooping up a portion. — This is the ultimate mac and cheese, we can thank the butternut squash for elevating everything about how this recipe tastes.

Like every recipe from the Crinkled Cookbook, this is scratch made and wow is it delicious. I love this recipe, and think you will too. The combination of roasted - or microwaved - butternut squash, three cheeses and chunky pasta creates classic comfort food that's a delicious, meatless main dish or an impressive side. It just takes four easy steps: cook the squash, make the cream sauce, cook the pasta and bake. You've got this!

Ingredients to have on hand

butternut squash
cheddar cheese
smoked gouda cheese
parmesan cheese
nutmeg
tabasco sauce
pasta

Diced butternut squash on a marble counter. — Dice the butternut squash into small, one or two inch cubes. Better yet, buy them from the grocery store this way.

Top Tips and FAQ

Can I use canned or frozen butternut squash?

Fortunately, there are plenty of options for getting to the interior of a butternut squash and either frozen or canned butternut squash will work. But I think the texture and flavor is far better in the butternut cheese sauce when we use fresh squash in this recipe.

I do like shortcuts though, and often buy the squash at the grocery store already cubed or peeled. But if you are willing to peel and cube a whole squash I offer tips on how to prepare a butternut squash in my recipe for Cookie Crumb Casserole.

Do I need to peel butternut squash before roasting it?

Leave the peel on. While I recommend using the microwave to cook and soften butternut squash, you can roast it in the oven as well. Very carefully slice the squash in half lengthwise and scoop out the seeds. Place the squash peel side down in a baking dish with a little water and bake at 350° F for about 90 minutes. The cooked squash will easily scoop out after it's baked.

Baked butternut squash, mashed lightly. — Bake the butternut squash until its softened. Then use a potato masher or a fork to create a semi-smooth consistency. A few lumps are fine!

Creamy, cheesy goodness abounds in this dish but it's the cooked butternut squash added to the cheese sauce that's the game changer. If you're wondering what you can add to mac and cheese to make it taste better, this recipe is it. I've made a lot of mac and cheese over the years and this recipe is my favorite way to prepare it.

Three types of grated cheese mounded on a cutting board. — Cheddar, smoked gouda and parmesan combine for a unique cheesy flavor that helps make this recipe a standout.

Three-Cheese Mac and Cheese

Mac and cheese is famous for including plenty of yummy cheddar cheese and this recipe is no exception. But here the combination of cheddar, along with smoked gouda and parmesan cheese improves the flavor. Smoked gouda has a richer flavor than regular gouda cheese and I think it's a great complement to the butternut squash.

Use Bite-Sized Pasta

I recommend using bite-sized pasta for this recipe. You'll want pasta that's in a shape that will be able to hold plenty of the creamy butternut cheese sauce in every bite. 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.

Pasta and cheese sauce in the pan, being stirred with a wooden spoon. — Use the same pot that you cooked the pasta in to make the cheese sauce. Then add the pasta back into the pan, stir and you are ready for the oven.

Use a baking dish that holds two quarts. A larger, glass baking dish works fine too, but the mac and cheese layer will be thinner and will cook faster. 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. — This dish is classic comfort food, be ready to accommodate second helpings!

Inspired by Trader Joe's

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.

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.

Making the Cream Sauce

The butternut cheese sauce in my recipe 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.

Shredded cheeses, butternut squash spices and cream sauce in a pan with a wise. — Blend the cheese, squash and spices with the hot cream sauce and whisk together off the stove, this will keep the milk and cheeses from scorching.

But I'm not one for being too fancy. Let's just add the cheese and the butternut squash and stir it up. Voila, a butternut cheese sauce.

Storing Leftovers and Freezer Tips

Store leftovers in a covered container in the refrigerator for 4-5 days. The cheese sauce tends to tighten up a bit when its 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.

This recipe will freeze well. Just keep in mind 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 it's original silky texture.

More Comfort Food Ideas

Here are a few more of my favorite comfort food recipes. Be sure to let me know what you think of these too! Share your rating by adding stars each time you cook something from the Crinkled Cookbook.

Blue Cheese and Rosemary Scalloped Potatoes

Turkey Pot Pie

The Best Jambalaya

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.

4.92 from 249 votes

Print Rate Pin Recipe

Prep Time: 40 minutes

Cook Time: 30 minutes

Total Time: 1 hour 10 minutes

Servings:

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.

Cook Butternut Squash

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.
Alternately, 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 in 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. It may take longer if the squash is very large. Once the squash is soft and tender, remove from the oven, cover with foil and cool slightly so it will be easier to handle. Using a large spoon, scoop out the baked squash and place in a bowl. Discard the peel.
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.

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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.

Pin Recipe

Butternut Squash Mac and Cheese

Ingredients to have on hand

Top Tips and FAQ

Three-Cheese Mac and Cheese

Use Bite-Sized Pasta

Inspired by Trader Joe's

Making the Cream Sauce

Storing Leftovers and Freezer Tips

More Comfort Food Ideas