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Baked Butternut Mac and Cheese

Made with three types of cheese, this baked Butternut Mac and Cheese recipe is ready in just 40 minutes! Perfect for family get togethers and holidays!

Two blue ramekins filled with three cheese butternut mac and cheese.

Creating This Butternut Squash Mac and Cheese Recipe

Gourmet mac and cheese is definitely comfort food in our home. I love this easy recipe for Baked Butternut Mac and Cheese — I can’t believe how many times we’ve made this in the last few months and I haven’t even shared it with you yet!

It was one of those quickly thrown together creations when I needed to get dinner on the table fast and was such a hit that we kept making it. I served it at Madeline’s school Christmas potluck and along with their parents, a bunch of 3- and 4-year-olds completely gobbled it up!

Now, you might be thinking — “Katie, how is this a quickly thrown together creation??” I hear you! But it really was quick and on the table within 30 minutes.

Ingredients for Butternut Mac and Cheese

This butternut squash gruyere mac and cheese is made completely from scratch, but comes together quickly. Here’s what you’ll need to make the recipe:

  • Pasta of choice (I used penne)
  • Yellow onion
  • Butter
  • All-purpose flour
  • Whole milk
  • Mascarpone
  • Gruyere cheese
  • Parmesan cheese
  • Spices (salt, pepper, cayenne, nutmeg)
  • Fresh rosemary
  • Butternut squash
  • Panko breadcrumbs

For the complete ingredient list and detailed instructions, scroll to the bottom of this post for the FREE printable recipe card.

How to Make Butternut Mac and Cheese

Homemade mac and cheese is easier to make than you might think! Here are the basic steps:

  1. Peel, remove the seeds, and cut the butternut squash into bite-sized cubes.
  2. Bring a pot of water to a boil and cook pasta 1 to 2 minutes less than the instructions tell you to.
  3. Add the squash to the pasta water during the last 3-5 minutes, depending on the size of your squash. Drain and set aside.
  4. In a large Dutch oven, melt the butter. Sauté the onion until soft and tender.
  5. Whisk in the flour and cook over medium heat till golden. Slowly whisk in the milk while cooking over medium heat.
  6. Add the spices. Stir in the mascarpone cheese, then whisk in the gruyere and parmesan until melted and creamy. Bring to a slow simmer, and then stir in the pasta and squash. 
  7. Transfer to an oven-safe casserole dish. Top with 1/2 cup of panko bread crumbs and bake at 400 degrees F until the pasta hot and the breadcrumbs are toasted.

The above is simply a quick summary of this recipe. Check out the free printable card at the bottom of this post for all the detailed instructions.

How Long to Bake Mac and Cheese?

Because the cheese sauce and squash is cooked prior to baking the mac and cheese, this particular recipe only needs to bake for about 10 to 20 minutes at 400ºF. You’ll know it’s done when the breadcrumbs are toasted and the cheese sauce is bubbling around the edges of the baking dish.

Two blue ramekins filled with three cheese butternut mac and cheese.

How Long Does Homemade Mac and Cheese Last?

You can keep this butternut squash mac and cheese in the fridge for up to five days. Store it in an airtight container for best results.

You can also freeze mac and cheese for up to three months. Let it cool completely before sealing in a freezer bag or freezer-safe container. When ready to eat, thaw overnight in the fridge.

Can I Use Different Types of Cheese?

Yes! Master the basic cheese sauce and utilize this recipe over and over again, but each time you can experiment with different cheeses. Adjusting and tweaking the flavors to fit your mood at the time.

In this recipe for butternut squash mac and cheese, gruyere is accented by mascarpone and Parmesan to create a rich, velvety sauce in this recipe. However, you can dream up infinite cheese combinations for your sauce.

Can I Add Other Mix-Ins?

Definitely! Adding accent meats and vegetables turns this homemade baked mac and cheese into a delicious, one-pot meal with lots of flavor and color.

I also like to add steamed broccoli or chopped spinach to my mac and cheese. My two favorite meat mix-ins are ham and bacon. They both go so well with cheesy sauce, but experiment with others as well.

Tips for Making Homemade Baked Mac and Cheese

  • Just because this is a “macaroni” and cheese recipe doesn’t mean you have to actually use macaroni pasta. In fact, I rarely do. I love shells, rotini, penne, wagon wheels and more for this butternut squash gruyere mac and cheese.
  • For quicker prep, purchase already prepared butternut squash from the grocery store. I like the pre-peeled, and chopped squash that Costco offers.
  • I recommend buying blocks of cheese and shredding them yourself. Pre-shredded cheese are often coated with anti-caking agents that make them slightly grainy once melted.

More Homemade Mac and Cheese Recipes:

This Bacon and Butternut Squash Mac and Cheese features penne covered in a creamy, rich sauce of pureed butternut squash, parmesan, and sharp white cheddar with bacon and fresh sage.

Jalapeño Bacon Mac and Cheese is loaded with poblano peppers, jalapeños, pepper jack cheese, and of course lots of bacon!

Macaroni and cheese stepped up a notch with asparagus, bacon and fancy cheeses including aged and sharp white cheddar cheeses. Asparagus Bacon Mac and Cheese? Yes, please!

Baked White Cheddar Mac and Cheese with Kale and Bacon is a bit sinful. Pasta loaded with rich, velvety cheese, kale, plenty of bacon, and a nice crispy topping.

I think you’ll agree that the ingredients in this Fontina, Spinach, and Bacon Shells and Cheese take your traditional shells and cheese to a whole new level.

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Baked Mac n Cheese with Gruyere and Butternut Squash

Baked Mac n Cheese with Gruyere and Butternut Squash

Yield: serves 6
Prep Time: 20 minutes
Cook Time: 20 minutes
Total Time: 40 minutes

Master a basic cheese sauce and utilize that recipe over and over again, but each time you can experiment with different cheeses. Adjusting and tweaking the flavors to fit your mood at the time.

Ingredients

  • 1 - 1 lb. box penne pasta
  • 1/2 of a yellow onion, diced
  • 3 tablespoons butter
  • 1/4 cup flour
  • 3 cups whole milk
  • 3 ounces mascarpone or cream cheese
  • 5 ounces gruyere cheese, grated
  • 1 ounce parmesan cheese, grated
  • 1/8 teaspoon nutmeg
  • 1/8 teaspoon cayenne pepper
  • 1/2 teaspoon black pepper
  • 1/2 to 1 teaspoon salt, according to personal preference
  • 1/4 - 1/2 teaspoon finely minced fresh rosemary
  • butternut squash, chopped into bite-sized pieces
  • 1/2 cup panko breadcrumbs

Instructions

  1. Peel, remove the seeds, and cut the butternut squash into bite-sized cubes, or however large you'd like them to be. Set aside.
  2. Bring a pot of water to a boil and cook pasta one to two minutes less than package instructions. Add the squash to the pasta water during the last 3-5 minutes, depending on the size of your squash. Drain and set aside.
  3. In a large French or Dutch oven, melt the butter. Saute the onion in the butter for 4-6 minutes, or until soft and tender. Whisk in the flour and cook over medium heat till golden. Slowly whisk in the milk while cooking over medium heat.
  4. Add the nutmeg, cayenne, black pepper, salt (if desired), and rosemary. Stir in the mascarpone cheese, whisking until melted and creamy. Then, whisk in the gruyere and parmesan until melted and creamy. Bring to a slow simmer, and then stir in the pasta and squash.
  5. Transfer to an oven-safe casserole dish. Top with 1/2 cup of panko bread crumbs and bake at 400 degrees F until the pasta is bubble and hot and the breadcrumbs are toasted, about 10-20 minutes. Serve immediately.

Notes

For quicker prep, purchase already prepared butternut squash from the grocery store. I like the pre-peeled, and chopped squash that Costco offers.

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Nutrition Information
Yield 6 Serving Size 1
Amount Per Serving Calories 501Total Fat 28gSaturated Fat 16gTrans Fat 0gUnsaturated Fat 9gCholesterol 82mgSodium 848mgCarbohydrates 42gFiber 2gSugar 8gProtein 20g

GoodLifeEats.com offers recipe nutritional information as a courtesy and is an estimate only. This information comes from online calculators. Although GoodLifeEats.com makes every effort to provide accurate information, these figures are only estimates.

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