If you want to elevate your mac and cheese game, then this Butternut Squash Mac and Cheese with Bacon is the answer! Creamy Gruyere and cheddar cheese come together with a mix of fresh herbs and subtle spices to make the most velvety smooth and flavor-packed sauce! You can serve this up for a fancy Fall side, or change up your traditional Thanksgiving menu with this impressive dish.

A wooden spoon digs into a pan of mac and cheese with butternut squash.

Best Butternut Squash Macaroni with Bacon

You know how sometimes things just fall perfectly into place?

Like the day you met your significant other. That time you hit all of the green lights on your way home from work. Or the concert tickets you miraculously won in a contest you didn’t even know you entered?!

That’s kind of how this butternut squash mac and cheese recipe was born.

What started with a craving for macaroni turned into inspiration. I saw a butternut squash about to go bad on my counter, a half packet of bacon in my refrigerator, and some fresh herbs I needed to use up.

And the rest? Sheer recipe magic.

What resulted was an explosion of the most savory, sweet, tangy, and umami flavors. The sweetness of the squash, the saltiness of the bacon, and the creaminess of the sauce is a showstopper. Creamy textures balanced out a crunchy bite.

It indeed has everything you’ve ever dreamed up in a macaroni and cheese—but made slightly healthier thanks to the addition of roasted butternut squash!

I’m very selective of the recipes I deem worthy of the Thanksgiving or Christmas table, but this one is going to make you look like a rockstar this holiday season and quickly become one of your favorite dishes.

(Looking for another butternut squash showstopper? You have to try Butternut Squash Risotto and Stuffed Butternut Squash.)

Butternut squash, noodles, milk, cheese, broth, and seasonings are the ingredients for this dish.

Ingredients

The ingredients needed for butternut squash mac and cheese include:

  • Butternut squash. You’ll need one pound of butternut squash that’s been peeled and cut into 1-inch cubes. You can also buy a bag of pre-cut butternut squash at the grocery store.
  • Oil. Both avocado oil and extra virgin olive oil will work in this recipe.
  • Seasonings. A blend of salt, black pepper, rosemary, sage, thyme, and nutmeg creates a rich flavor for this dish.
  • Pasta. You can use any type of pasta, but elbows are the typical choice. Choose either gluten-free noodles or regular wheat pasta. Chickpea pasta or lentil pasta are healthier alternatives, as well.
  • Bacon. Everything is better with bacon. The recipe calls for 5 ounces of bacon cut into ½-inch pieces.
  • Shallots. Finely chopped shallots are used to create layers of flavor in this pasta.
  • Garlic. Similar to the shallots, fresh minced garlic is sautéed to create a rich base. Powdered is less than ideal but will work in a pinch.
  • Flour. Choose either an all-purpose or a gluten-free 1-to-1 blend.
  • Liquid. You will need both broth (either chicken or vegetable) and milk.
  • Cheese. The essential ingredients! Multiple kinds of cheese are used in this sauce. Sharp cheddar and Gruyere were tested, but you can change it up if needed. Parmesan cheese is mixed with breadcrumbs for a topping.
  • Breadcrumbs. You can opt for gluten-free or regular Panko-style breadcrumbs for a crispy topping.
  • Butter. You only need a little for the topping. If needed, you can substitute oil.

How to Make Butternut Squash Mac and Cheese

Below are the step-by-step instructions to follow to make this butternut squash mac and cheese at home:

Roast the Butternut Squash

Preheat the oven to 425℉.

Learn How to Peel and Cut Butternut Squash.

Then, toss the squash into a 9×13-inch baking dish and drizzle oil over it. Sprinkle 1 teaspoon salt and ¼ teaspoon black pepper. Stir to coat all of the pieces evenly.

Bake in the preheated oven for 22 to 25 minutes, just until tender.

Cubed butternut squash in a white casserole dish ready for the oven.

Purée the Squash

After it is roasted, it’s time to purée the cooked squash. 

Add it to a large high-speed blender or a food processor. Toss in 2 teaspoons of the fresh herbs and nutmeg.

Blend for 1 to 2 minutes. You want a smooth consistency without any clumps. Set it aside.

Prepare the Pasta

Pour the noodles into a large pot of water, then boil the pasta according to the package instructions.

After it is cooked to al dente, drain the noodles in a colander and set aside.

Tip: Drizzle some olive oil over the pasta and toss so it doesn’t stick together.

Cook the Bacon and Shallots

Add the cut bacon pieces to a Dutch oven or large saucepan. Cook for around 7 to 8 minutes over medium-high heat, just until it’s crispy. (Learn more about how to cook bacon!)

Use a slotted spoon to remove the bacon from the pot and drain it on a paper towel. Then, remove the bacon grease from the pot and use a paper towel to wipe out any burned bits.

Return 1 tablespoon of grease to the pot along with the diced shallots. Cook for 2 to 3 minutes, until they’re tender.

Then, add the minced garlic and cook for another 30 seconds.

Make the Cheese Sauce

Sprinkle the flour over the mixture, then whisk until it forms a paste. Pour ½-cup of the broth into the pot quickly, and mix to combine. As the sauce thickens, carefully add the rest of the broth and milk, ½-cup at a time, being sure to whisk well after each addition.

Then, stir the cheese, puréed squash, and cooked macaroni into the ultra-creamy sauce. Stir well.

Top the Macaroni

Carefully pour the macaroni and cheese mixture into the 9×13-inch dish you used earlier. Sprinkle the cooked bacon pieces on top of the macaroni noodles and butternut cheese sauce.

Stir the melted butter, breadcrumbs, and Parmesan cheese together in a small bowl. Spread the mixture evenly over the pasta.

Bake in the Oven

Reduce the oven temperature to 375℉. Bake the pasta for 25 to 30 minutes, or just until the topping begins to turn golden brown.

If you want a crispy topping, broil for an extra 1 to 2 minutes.

Let the mac and cheese rest for 5 to 10 minutes so the sauce can thicken before serving this creamy goodness.

A wooden spoon digs into a pan of mac and cheese with butternut squash.

Meal Prep and Storage

  • How to prep ahead of time: You can cook the bacon and the pasta a day or two early. Or, completely make the mac and cheese, but wrap and place in the fridge just before baking.
  • How to store: Save mac and cheese leftovers in an airtight container in the fridge for up to 4 to 5 days.
  • How to freeze: For the best results, freeze the macaroni and cheese before baking in the oven.
  • How to reheat: Warm the mac and cheese back up in the oven or in the microwave with a little extra milk for a creamy consistency.

Is butternut squash mac and cheese healthy?

Macaroni and cheese in general is not healthy, but the addition of butternut squash provides some marginal benefits. Butternut squash contains potassium, vitamin C, and fiber, which improves the overall nutritional value of mac and cheese.

What to serve with butternut squash mac and cheese?

Serve this delicious macaroni and cheese with your favorite protein, like chicken, pork, or even steak. It’s delicious anywhere you would enjoy traditional mac and cheese.

Dietary Modifications

Here are some adjustments and substitutions you can make to help this recipe fit your dietary requirements:

  • Gluten-free: Choose a gluten-free pasta and breadcrumbs along with a gluten-free 1-to-1 flour blend.
  • Vegetarian: Skip the bacon.
  • Dairy-free: Stick with dairy-free milk and cheese.
Butternut squash mac and cheese is a creamy and delicious side dish.

Expert Tips and Tricks

  • Save time. Grab some pre-cut butternut squash from the store rather than peeling and cutting your own.
  • Change it up. You can stick with cheddar and Gruyere, or choose another type of cheese.
  • Make it work. Choose ingredients that work for your diet plan, either gluten-free, or dairy-free.
  • Top it off. The bacon, cheese, and breadcrumbs sprinkled over the pasta make it so delicious.
  • Serve it up. This dish is ideal with lean chicken or fish.

Other Butternut Squash Recipes

If your garden is brimming with this versatile vegetable, or you just love it, try any of these recipes next.

Roasted Butternut Squash Soup is irresistible in the cooler months.

Butternut Squash Risotto is super impressive. And Sausage and Sage Stuffed Butternut Squash is so delicious.

Or, keep it simple with Mashed Butternut Squash, Roasted Butternut Squash Cubes or Air Fryer Butternut Squash.

More Thanksgiving Side Dish Recipes

Thanksgiving is always made better by the side dishes. Be sure to put these on your menu.

You can’t go wrong with Sweet Potato Casserole and Cajun Cornbread Casserole.

Other classics like Instant Pot Mashed Potatoes and Green Bean Casserole are always favorites.

Check out a whole list of Thanksgiving Sides

Tap stars to rate!

5 from 3 votes

Butternut Squash Mac and Cheese with Bacon

If you want to elevate your mac and cheese game, then this Butternut Squash Mac and Cheese with Bacon is the answer! Creamy Gruyere and cheddar cheese come together with a mix of fresh herbs and subtle spices to make the most velvety smooth and flavor-packed sauce.
A wooden spoon digs into a pan of mac and cheese with butternut squash.
Yield 8 servings
Prep 45 minutes
Cook 30 minutes
Total 1 hour 15 minutes
An image of an envelope sealed shut with the Evolving Table logo.

Email this recipe!

Enter your email and we’ll send it directly to you.

Ingredients 

  • 1 lb. butternut squash peeled, ½ to 1-inch cubes
  • 1 Tbsp. oil olive or avocado
  • 2 ½ tsp. salt divided
  • ½ tsp. black pepper divided
  • 2 tsp. rosemary sage, and/or thyme, fresh, finely chopped
  • tsp. nutmeg ground
  • 12 oz. pasta elbows, gluten-free if needed
  • 5 oz. bacon cut into ½-inch pieces
  • 2 shallots finely chopped
  • 2 cloves garlic finely minced
  • ¼ cup flour all purpose or a gluten-free 1-to-1 blend
  • 1 ½ cups broth chicken or vegetable, divided
  • 1 ½ cups milk regular or plant-based
  • 1 cup Cheddar cheese shredded
  • 1 cup Gruyere cheese shredded
  • cup Panko breadcrumbs gluten-free if needed
  • ¼ cup Parmesan cheese grated
  • 1 Tbsp. butter

Instructions 

  • Preheat the oven to 425 degrees.
  • Roast Butternut Squash: Add the butternut squash cubes to a 9×13-inch baking dish. Drizzle with oil and sprinkle with 1 teaspoon salt and ¼ teaspoon black pepper. Toss to coat and then roast in the preheated oven for 22-25 minutes, or until tender.
    1 lb. butternut squash, 1 Tbsp. oil, 2 ½ tsp. salt, ½ tsp. black pepper
  • Puree Squash: Once roasted, add to a large high-speed blender or food processor along with 2 teaspoons of fresh herbs and nutmeg. Blend for 1-2 minutes, or until smooth and no clumps remain. Set aside until ready to use.
    2 tsp. rosemary, ⅛ tsp. nutmeg
  • Boil Macaroni: Boil pasta in a large pot according to package directions. Drain in a colander and set aside. (Optional: drizzle a tablespoon of oil over the pasta and toss to combine to prevent it from clumping together while it cools.)
    12 oz. pasta
  • Cook Bacon and Shallots: Add bacon pieces to a Dutch oven or large skillet over medium-high heat and cook for 7-8 minutes, or until crispy. Remove the bacon from the skillet using a slotted spoon and let drain on a paper towel-lined plate. Remove the bacon grease from the Dutch oven, wipe out any burnt bits, and pour back in 1 tablespoon of grease. Add the diced shallots and cook for 2-3 minutes, or until tender. Add the minced garlic and cook for 30 seconds, or until fragrant.
    5 oz. bacon, 2 shallots, 2 cloves garlic
  • Make the Butternut Squash & Cheese Sauce: Whisk in flour until it thickens and forms a paste. Quickly pour in ½ cup broth, mixing to combine. Slowly add in the remaining broth and milk, ½ cup at a time, whisking well after each addition. Wait until the sauce thickens before pouring in the next amount. Add the cheese, pureed squash, and cooked pasta to the sauce. Stir until well combined.
    ¼ cup flour, 1 ½ cups broth, 1 ½ cups milk, 1 cup Cheddar cheese, 1 cup Gruyere cheese
  • Add Macaroni to Baking Dish: Pour the macaroni and cheese into the previously used 9×13-inch baking dish and top with the cooked bacon pieces. In a small bowl, toss together the melted butter, breadcrumbs, and Parmesan cheese. Sprinkle the topping over the pasta.
    ⅓ cup Panko breadcrumbs, ¼ cup Parmesan cheese, 1 Tbsp. butter
  • Bake in Oven: Reduce the oven temperature to 375 degrees and bake for 25-30 minutes, or until the topping begins to brown. (Optional: broil for an additional 1-2 minutes.) Let sit for 5-10 minutes so the sauce can thicken up and then serve with additional fresh herbs.
Last step! If you make this, please leave a review letting us know how it was!

Tap stars to rate!

5 from 3 votes

Video

Notes

Meal Prep and Storage

  • How to prep ahead of time: You can cook the bacon and the pasta a day or two early. Or, completely make the pasta, but wrap and place in the fridge just before baking.
  • How to store: Save mac and cheese leftovers in an airtight container in the fridge for up to 4 to 5 days.
  • How to freeze: For the best results, freeze the macaroni and cheese before baking in the oven.
  • How to reheat: Warming the mac and cheese back up in the oven or in the microwave with a little extra milk for a creamy consistency.
  •  
  •  
  •  

Nutrition

Calories: 484kcal, Carbohydrates: 51g, Protein: 19g, Fat: 23g, Saturated Fat: 10g, Polyunsaturated Fat: 3g, Monounsaturated Fat: 8g, Trans Fat: 0.1g, Cholesterol: 50mg, Sodium: 1209mg, Potassium: 424mg, Fiber: 4g, Sugar: 7g, Vitamin A: 6629IU, Vitamin C: 13mg, Calcium: 434mg, Iron: 2mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Made this recipe?Leave a comment below!
5 Secrets to Healthier Family Dinners
Tips & recipes for getting yummy — and healthy — meals on the table.

You May Also Like

Thanks for
Stopping By!

I’m London! Join me as we cook up nourishing meals for you and your loved ones and learn a few healthy cooking tips and tricks!

Leave a comment

Your email address will not be published. Required fields are marked *

Recipe Rating