Butternut Squash Mac and Cheese

Butternut Squash Mac and Cheese

Last Updated on September 28, 2023 by Jacqueline Rafidi

Butternut squash Mac and cheese seems to be a staple this time of year. And this butternut squash mac and cheese is SO similar to the Trader Joe’s one that makes an appearance in the freezer section every fall. If you live in the states and near a Trader Joe’s, you’re bound to know about their infamous butternut squash mac and cheese. I created this recipe with that dish in mind – the flavors are warm and the sauce is so luscious. 

Butternut Squash Mac and Cheese

And sure this butternut mac may be my take on the original, but it still has my own twist on it. I love butternut squash in tons of recipes. Take this butternut squash risottoTurkey, butternut squash and béchamel lasagna rolls, and this coming week, I also have a fall white bean and kale minestrone soup featuring this veggie. Since this special veggie will be featured in the grocery store the next coming months, this gives you some ideas on what to do with it!

Making this butternut squash mac and cheese is easy

The first step to creating the most flavor is roasting a medium butternut squash. Carefully remove the skin, scoop out the seeds (reserve these to roast up later or save for gardening) and dice up the squash flesh into small cubes. The smaller the cubes, the faster they’ll roast, but cooking time does vary.

I love roasting it on a baking sheet with olive oil and all the spices. This way, the spices have a chance to warm up and become more fragrant and flavorful. This step really sets this butternut squash mac and cheese recipe apart from the rest! It’s a great way to start building flavor right away. I add things like onion powder, garlic powder, paprika for color, poultry seasoning and other warm spices. Let it roast about 40 minutes, give or take 

Butternut Squash Mac and Cheese

Once the butternut squash is fork tender, remove it from the oven and let it cool while the pasta cooks to package directions in a large pot of salted water. Shred up your gouda, white cheddar and Parmigiano Reggiano. It’s important to grate up the cheeses yourself so they can melt more evenly and just gives it an overall better flavor. Once the pasta is al dente, reserve 2 cups of the pasta water which helps the butternut cheese sauce thicken without adding corn starch or flour. Drain the pasta from the remaining water and set the pasta aside.

Butternut Squash Mac and Cheese

Once the squash is cooled, add it to a blender or food processor with the milk and blend to desired consistency until smooth and creamy. I find this process works the best and you end up with the best texture! You could also try using a fork or potato masher or even an immersion blender in the skillet – just be sure its not a non-stick pan so nothing scratches. 

Add the pureed butternut squash mixture to a large skillet on medium-low heat, top with the pasta then alternate between the cheeses and the pasta water to let the cheese melt and develop a luscious and delicious final butternut squash cheese sauce.

This has quickly become one of my favorite pasta recipes in the fall months and for a good reason! The sweetness of the squash pairs so well with the saltiness of the cheeses and the warm spices just makes this butternut squash mac and cheese feel all cozy which we love.

Butternut Squash Mac and Cheese

Before serving, I love topping it with more cheese and a sprinkle of red pepper flakes for added heat (you could also add some red pepper flakes or cayenne to the sauce for an extra kick! 

I know you’re going to love this version of mac and cheese and my take on the Trader Joes butternut squash mac and cheese which is one of my faves every fall. Mac and cheese is often a hit with kids, and with all the cheesy goodness in this recipe, it’s bound to be a hit for the whole family. Let me know if you give this recipe a try!

Find the step-by-step instructions in the recipe card below. And of course, modify it to your liking or your dietary needs. If you want to make this a vegan butternut squash mac and cheese, switch the whole milk for cashew milk, almond milk or any other non dairy milk of choice and replace with any vegan cheese you like and a gluten-free pasta if desired. The main component you’ll want is that creamy sauce for your pasta and luckily there are tons of quality vegan alternatives.

To me, the best part of any meal is enjoying the leftovers! I love being able to grab some cozy comfort food like this, warm it up on the stove and enjoy. Especially once the weather cools off. Store any leftovers in an airtight container in the fridge for about 3-5 days. 

Here are some of my other fall favorite recipes

Butternut squash risotto
Turkey Pumpkin Chili
Mexican chicken and rice soup
Turkey, butternut squash, bechamel lasagna rolls
Pumpkin butter white russian

When you make this butternut squash mac and cheese, comment down below and rate this recipe to let me know your thoughts! Also share a picture or tag me on Instagram @thebitewithjackie, I love seeing your remakes!

Butternut Squash Mac and Cheese

Butternut Squash Mac and Cheese

A creamy pasta with warm spices reminiscent of the famous Trader Joes version
Prep Time 10 minutes
Cook Time 1 hour
Total Time 1 hour 10 minutes
Course Main Course
Cuisine American
Servings 4


  • Blender, food processor, or immersion blender recommended


  • 1 butternut squash peeled and diced, about 3 ½ – 4 cups
  • 3 Tablespoons extra virgin olive oil
  • 1 teaspoon poultry seasoning
  • 1 teaspoon onion powder
  • 1 teaspoon garlic powder
  • 1 teaspoon paprika
  • ½ teaspoon dried sage
  • ½ teaspoon dried thyme
  • ¼ teaspoon nutmeg
  • ¼ teaspoon cayenne optional for a spicier kick
  • Salt and pepper to taste
  • 2 – 2 ½ cups whole milk or milk of choice
  • 1 box pasta of choice I use rigatoni or mezze rigatoni
  • 1 cup gouda cheese shredded
  • ½ cup white cheddar cheese shredded
  • ½ cup Parmigiano Reggiano grated
  • Red pepper flakes optional for topping


  • Preheat the oven to 400F
  • Add all your diced butternut squash to a baking tray, drizzle with the olive oil and add all your spices, salt and pepper so all the squash is coated evenly. Roast for 30-40 minutes or until fork tender. While the squash roasts, bring a large pot of salted water to a boil and then shred all your cheeses. When the butternut squash is done remove from the oven and add the pasta to the boiling water and cook until al dente reserving 1 ½ – 2 cups of the pasta water.
  • Add the butternut squash and the milk to a blender or processing equipment of choice. (If you don’t have one, you could also use a fork to very finely mash up the butternut squash by hand, but I do find that blending makes the sauce turn out much smoother.) Once blended and to a pan over medium low heat then add the pasta directly to the sauce. Top the pasta with 1/3 of the cheese and mix gently. Add about 2-3 Tablespoons of the pasta water and mix. Repeat these steps until all the cheese is finished, leaving a bit for garnish, and the consistency is how you like it.
  • Serve with topped with the remaining cheese and a sprinkle of red pepper flakes. Enjoy!
Keyword Butternut Squash, Butternut Squash Mac and Cheese, Fall Recipes

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