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.

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
Top Tips and FAQ
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.
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.
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-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.
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.
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.
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
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?
Melinda O'Malley Keckler says
Hello! Please DO cook the pasta first. 🙂
Daisy Songbird says
You need to read the recipe. It tells you to cook the pasta!
Mama Maggie's Kitchen says
I bet this is as good as it looks. YUMMMM!
Chef Dennis says
This is making me hungry!
Kayla DiMaggio says
Yum! I love butternut squash and the smoked gouda cheese in the dish was so delicious!
Jeannie says
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.