This Butternut Squash Mac & Cheese recipe is the ultimate creamy, cheesy comfort food that every family craves in the fall. It takes classic mac and cheese and adds a simple, healthy twist by incorporating rich, velvety butternut squash puree into the sauce. This technique not only boosts the nutritional value but also creates an incredibly decadent texture, making it the perfect hearty weeknight meal or an impressive, wholesome side dish for your holiday table.

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Why You'll Want to Make Butternut Squash Mac & Cheese
- A Hidden Veggie Boost: The butternut squash completely replaces the need for a flour-based roux, giving you a smooth, thick sauce that's packed with vitamins and fiber-without sacrificing any of the cheesy flavor.
- The Best Texture: Using a combination of Extra Sharp Cheddar Cheese for flavor and a touch of Goat Cheese for tang ensures a luxurious, ultra-creamy, and smooth sauce every time.
- Perfect for Holidays: It's a wonderful alternative to heavy casseroles. Serve it as a Vegetarian main dish or as a beloved side for Thanksgiving, Christmas, or a fun, family-friendly meal for Halloween weekend.
- Ready in Under an Hour: With a total time of just 35 minutes, this recipe is easy enough for any busy evening.
Ingredients - Here's What You'll Need

Steps to Make Butternut Squash Mac & Cheese
- Bring a large pot of well-salted water to boil over high heat. While you're waiting for the water to boil, combine the frozen butternut squash and ¼ cup of water in a large skillet with a lid, set over medium-high heat. (I used my large 5-quart Le Creuset Braiser.) Place the lid on the pan and cook, stirring occasionally, for 5 to 7 minutes. Then, uncover and cook for 2 to 3 minutes, stirring constantly, until all the water has evaporated.

- Add cubed unsalted butter, freshly ground black pepper, and Kosher salt and stir until the butter is melted.

- Then, add the all-purpose flour and stir to incorporate. Cook stirring constantly, until the squash mixture has thickened, for about 2 to 3 minutes.

- Gradually add the milk, about ½ a cup at a time, stirring constantly, until all of the milk has been incorporated.

- Add the freshly minced thyme, garlic powder, and cayenne pepper, then bring to a simmer.

- Add the goat cheese and extra sharp cheddar cheese, then stir constantly until all of the cheese is melted and well incorporated. Remove from the heat and allow to cool for about five minutes.

- When the sauce mixture has cooled slightly, transfer all of it to a large four-cup measuring cup, and clean the pan to ensure none of the chunky sauce mixture remains. Then, process the sauce in the blender in two batches until it's smooth and creamy. Return the first batch to the cleaned pan, then set the pan over medium-low heat. Leave the second batch in the blender until ready to incorporate it with the pasta.

- Once the salted water begins to boil, add the dry shells pasta and cook according to package directions minus three minutes from al dente.

- When the pasta is almost done reserve about a cup of the pasta water.

- Drain the pasta in a colander set in the kitchen sink. Then, add the drained pasta to the sauce in the pan and stir the pasta into the sauce.

- Add the remaining sauce and stir so the all the pasta is well coated.

- Ladle in about ½ cup of the reserved pasta water and stir it into the Mac & Cheese. Remove the pan from the heat and let it cool for about five minutes.

- If the sauce is too thick, add some of the remaining water until the desired consistency is reached.

This Butternut Squash Mac and Cheese is the ultimate proof that comfort food can also be wholesome. Whether you're looking for a clever way to sneak a veggie into a kid-friendly dinner or planning your holiday menu, this recipe delivers a satisfying depth of flavor that will warm you from the inside out. Don't wait for a cool evening-try this creamy cheesy pasta tonight and let us know what you think of this healthy twist on a classic!

Frequently Asked Questions
Absolutely! If using fresh, simply peel and cube a small to medium-sized squash, roast it with a drizzle of olive oil until tender (about 30-40 minutes at 400°F), and then blend it into a smooth puree before adding it to your sauce.
Store leftovers in an airtight container in the refrigerator for up to 4 days. To reheat, place the mac and cheese in a pot on the stove over low heat. Add a splash of milk or chicken broth and stir constantly until creamy and heated through. This prevents it from drying out.
If you want a similar tang and richness, you can substitute the goat cheese with an equal amount of softened cream cheese or Mascarpone cheese.
Short, sturdy, and ridged pasta shapes work best because they hold onto the thick, creamy sauce. Excellent choices include shells (as listed), elbow macaroni, cavatappi, or rotini. The ridges and cups ensure that every bite is loaded with the butternut squash cheese sauce.
Recipe Tips and Tricks
- Milk Temperature Matters: Always add Whole Milk (or half-and-half) to your cheese slowly and ensure it is warm or room temperature. Adding cold milk to hot cheese can cause the sauce to seize or become grainy.
- Use Freshly Grated Cheese: Pre-shredded cheese is coated with anti-caking agents that prevent it from melting smoothly. For the creamiest results, buy a block and shred the Extra Sharp Cheddar Cheese yourself.
- Flavor Boost: Don't skip the Fresh Thyme. It provides an earthy, autumnal aroma that elevates the entire dish and pairs beautifully with the squash.
- Prevent a Broken Sauce: Once you add the cheese, keep the heat low-do not let the sauce boil. High heat causes the fat and protein in the cheese to separate, resulting in a greasy, clumpy sauce. Stir until the cheese is just melted and smooth, then immediately remove it from the heat.
Other Great Side Dishes
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Butternut Squash Mac & Cheese
Equipment
- Large Skillet with a Lid1
- Blender
- Large Pasta Pot
Ingredients
- 20 oz Frozen Butternut Squash
- ¼ c Water
- 4 tbs Unsalted Butter cubed
- ½ teaspoon Freshly Ground Black Pepper
- 1 tsp Kosher Salt
- ¼ c All-Purpose Flour
- 2 c Whole Milk
- 1 teaspoon Fresh Thyme minced
- ½ teaspoon Garlic Powder
- pinch Cayenne Pepper
- 4 oz Goat Cheese
- 4 oz Extra Sharp Cheddar Cheese
- 1 lb Medium Pasta Shells
Instructions
- Bring a large pot of well-salted water to boil over high heat.2 Once the salted water begins to boil, add the dry shells pasta and cook according to package directions minus three minutes from al dente. When the pasta is almost done, reserve about a cup of the pasta water. Drain the pasta in a colander set in the kitchen sink.
- In a large skillet with a lid, set over medium-high heat, combine the frozen butternut squash and ¼ cup of water. Place the lid on the pan and cook, stirring occasionally, for 5 to 7 minutes. Then, uncover and cook for 2 to 3 minutes, stirring constantly, until all of the water has evaporated.
- Add cubed unsalted butter, freshly ground black pepper, and Kosher salt and stir until the butter is melted.
- Then, add the all-purpose flour and stir to incorporate. Cook, stirring constantly, until the squash mixture has thickened, for about 2 to 3 minutes.
- Gradually add the milk, about ½ a cup at a time, stirring constantly, until all of the milk has been incorporated.
- Add the freshly minced thyme, garlic powder, and cayenne pepper, then bring to a simmer.
- Add the goat cheese and extra sharp cheddar cheese, then stir constantly until all of the cheese is melted and well incorporated. Remove from the heat and allow to cool for about five minutes.
- When the sauce mixture has cooled slightly, transfer it to a large four-cup measuring cup and clean the pan to ensure none of the chunky sauce mixture remains. Then, process the sauce in the blender in two batches until it's smooth and creamy. Return the first batch to the cleaned pan, then set the pan over medium-low heat. Leave the second batch in the blender until ready to incorporate it with the pasta.
- Add the drained pasta to the sauce in the pan and stir the pasta into the sauce. Add the remaining sauce and stir so the all the pasta is well coated. Ladle in about ½ cup of the reserved pasta water and stir it into the Mac & Cheese. Remove the pan from the heat and let it cool for about five minutes. If the sauce is too thick, add some of the remaining water until the desired consistency is reached.
- Yield 8 servings
Tips/Notes
- I used my large 5-quart Le Creuset Braiser.
- Begin cooking the sauce while you're waiting for the pasta water to boil. They should both be done around the same time.














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