Cheesy Baked Butternut Squash Mac and Cheese
Cheesy Baked Butternut Squash Mac and Cheese is a delightful twist on the classic comfort dish that we all know and love. This creamy, cheesy pasta goes beyond mere indulgence, incorporating the subtle sweetness of roasted butternut squash that is not only delicious but also packs a nutritional punch. Imagine a bowl brimming with tender shells, enveloped in a luscious cheese sauce that balances sharp cheddar with the nutty richness of Gruyere. It’s not just a meal; it’s an experience that warms the heart and soul.
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I first stumbled upon this enchanting combination at a cozy autumn gathering where the host served it as a side dish. Instantly enchanted, I knew I had to recreate it in my kitchen. It’s not only easy to make, but it also transforms ordinary ingredients into something extraordinary. Perfect for weeknight dinners or special occasions, this Cheesy Baked Butternut Squash Mac and Cheese will certainly win over even the pickiest eaters. So, whether you’re hosting a gathering or just looking for a comforting meal at home, this recipe is a warm invitation for you to explore.
Why You’ll Love This Recipe
- Simple & Quick: With just a 20-minute prep time and an 80-minute cooking time, it’s an easy dish to whip up in a hurry.
- Irresistible Flavor: The combination of roasted squash and three types of cheese creates a creamy, dreamy flavor profile that’s both comforting and sophisticated.
- Eye-Catching Appeal: The vibrant color of the butternut squash makes this dish a feast for the eyes, sure to impress your guests.
- Flexible Serving: Whether it’s a cozy family meal, a holiday gathering, or even a potluck, this mac and cheese is a perfect fit for any occasion.
- Diet-Friendly Options: You can easily adapt this to be gluten-free with specific pasta choices, making it a versatile option for various dietary needs.

Ingredients You’ll Need
- 1 large butternut squash: The star ingredient, adding natural sweetness and a creamy texture. Look for a squash that feels heavy for its size.
- 2 shallots, roughly chopped (⅔ cup): These bring a mild onion flavor; you can substitute with regular onions if needed.
- 1 pound shell pasta, or pipette rigate or elbows: Choose your favorite pasta; the shapes hold the cheese sauce well.
- ¼ cup extra-virgin olive oil: Used for roasting the squash and shallots, adding richness to the dish.
- 2 teaspoons balsamic vinegar: This brightens the flavors and complements the sweetness of the squash; feel free to swap with red wine vinegar.
- 1½ teaspoons sea salt: Essential for flavor, use kosher salt if preferred for its texture.
- 1 teaspoon onion powder: Adds depth and a hint of sweetness.
- ½ teaspoon garlic powder: Offers a subtle garlic flavor without the bites of fresh.
- ½ teaspoon ground sage: This herb brings a warm, earthy touch; substitute with thyme if desired.
- ¼ teaspoon nutmeg: A pinch elevates the dish to comfort food perfection.
- Freshly ground black pepper: For seasoning, always taste and adjust.
- 1½ cups unsweetened almond milk: This dairy-free option keeps the sauce creamy; regular milk can also be used.
- 6 ounces grated sharp cheddar cheese (about 2½ cups): A must-have for that classic mac and cheese flavor.
- 6 ounces grated gruyere cheese (about 2½ cups): Brings a nutty taste and makes the sauce extra creamy.
- 1½ ounces finely grated pecorino cheese (½ cup): This cheese adds a salty punch at the finish.
- ¾ cup panko breadcrumbs: For a crispy topping; you can substitute with regular breadcrumbs.
- 1½ teaspoons extra-virgin olive oil: Mixed with panko for extra flavor and crispiness.
How to Make Cheesy Baked Butternut Squash Mac and Cheese
Preheat: Start by preheating your oven to 425°F (220°C). Lines your baking sheet with parchment paper and greases a 9×13-inch baking dish to keep cleanup easy.
Prepare the Squash: Slice the butternut squash in half lengthwise and scoop out the seeds. Drizzle the cut sides with olive oil and sprinkle with sea salt and freshly ground black pepper. Place the squash cut side down on the baking sheet. For the shallots, wrap them in foil, drizzle with olive oil, season with salt, and then place on the baking sheet. Roast everything for about 30 to 45 minutes, or until the squash is tender and easily pierced with a fork.
Make the Topping: While the squash and shallots roast, combine ¾ cup panko breadcrumbs with 1½ teaspoons of olive oil in a small bowl. Toss until evenly coated; this will create a deliciously crunchy topping.
Cook the Pasta: Fill a large pot with salted water and bring it to a boil. Cook 1 pound of shell pasta according to package instructions until al dente. Don’t forget to scoop out 1½ cups of the starchy pasta water just before draining.
Blend the Sauce: Measure 2 cups of the roasted squash flesh and place it in a blender along with the reserved pasta water, the roasted shallots, ¼ cup olive oil, 2 teaspoons balsamic vinegar, 1½ teaspoons sea salt, 1 teaspoon onion powder, ½ teaspoon garlic powder, ½ teaspoon ground sage, ¼ teaspoon nutmeg, and several grinds of black pepper. Blend until creamy; this savory mixture will become the heart of your mac and cheese.
Cook & Combine: Return the empty pasta pot to the stove and heat the 1½ cups almond milk over medium heat. Stir in the blended squash sauce and let it warm through for about 3 minutes, stirring frequently. Gradually whisk in the 6 ounces of grated sharp cheddar cheese, the 6 ounces of grated Gruyere cheese, and 1½ ounces of finely grated pecorino cheese, making sure each addition is perfectly melted before adding the next. The result should be a creamy, cheesy sauce that coats every piece of pasta beautifully. Then, add the cooked pasta to the pot and stir until well combined.
Broil for Texture: Preheat your oven broiler. Carefully transfer the cheesy pasta mixture to the greased baking dish and sprinkle the panko topping evenly across the top. Broil for 5 to 10 minutes, watching closely until the topping is crisp and golden brown, with bubbling edges.
Rest & Serve: Once baked, be sure to let your Cheesy Baked Butternut Squash Mac and Cheese stand for about 15 minutes before serving. This waiting time allows the flavors to settle and the dish to firm up a bit for easier serving.

Storing & Reheating
To keep your cheesy delight fresh, let it cool and then store it at room temperature for up to 2 hours. For longer storage, refrigerate in an airtight container for up to 4 days. If you want to freeze it, portion it out in freezer-safe containers for up to 3 months. When you’re ready to enjoy, simply reheat in the oven or microwave. Note that the texture may change slightly, but a splash of almond milk as you reheat will help refresh the creaminess.
Chef’s Helpful Tips
- Keep an eye on the squash while roasting, as larger pieces may take a bit longer to become tender.
- To prevent the sauce from being too thick, don’t hesitate to add more pasta water or almond milk as you stir the cheese in.
- Feel free to experiment with different cheeses based on your taste preference; mozzarella or fontina can also create wonderful textures.
- This dish is great for make-ahead meals. Assemble it the day before and just pop it in the oven when you’re ready to eat.
- For added flair, you can mix in cooked spinach or kale for a pop of color and nutrients.
While this Cheesy Baked Butternut Squash Mac and Cheese is undeniably a star on its own, there’s something about its warmth and comfort that calls for sharing. Its rich flavors, creamy texture, and vibrant appearance create a dish that not only satisfies but also delights at any gathering. Feel free to make this your own – play with additional spices, or toss in some veggies. It’s all about enjoying the process and sharing the love through food!
Recipe FAQs
Can I use a different type of pasta?
Absolutely! While shell pasta, pipe rigate, or elbows work wonderfully, feel free to use your favorite pasta shape. Just ensure it’s a type that holds the cheese sauce well. Gluten-free pasta can also be used without compromising flavor.
How can I make it dairy-free?
To keep this dish dairy-free, use unsweetened almond milk and swap the cheeses for vegan cheese options. Many brands offer deliciously creamy alternatives that melt nicely.
Can I prepare it in advance?
Definitely! Assemble the dish up to the broiling step a day ahead. Store it covered in the refrigerator, then just pop it in the oven when you’re ready to bake. Adjust the broiling time, as the dish will be cold coming from the fridge.
What can I serve with it?
This Cheesy Baked Butternut Squash Mac and Cheese pairs beautifully with a fresh green salad or roasted vegetables. For a heartier meal, consider serving it alongside some grilled chicken or juicy pork chops. The flavor balance will complement the creamy pasta wonderfully!
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📖 Recipe Card

Cheesy Baked Butternut Squash Mac and Cheese
- Prep Time: 20 minutes
- Cook Time: 80 minutes
- Total Time: 1 hour 40 minutes
- Yield: 8 servings 1x
- Category: Main Dishes
- Method: Baking
- Cuisine: American
Description
This Cheesy Baked Butternut Squash Mac and Cheese is a delicious twist on a classic. Creamy, cheesy, and packed with flavor from roasted butternut squash, it’s an ideal comfort food for any dinner. Easy to prepare, it combines delectable cheese varieties with nutritious ingredients for a fulfilling meal.
Ingredients
- 1 large butternut squash
- 2 shallots, roughly chopped (⅔ cup)
- 1 pound shell pasta, or pipe rigate or elbows
- ¼ cup extra-virgin olive oil, plus more for drizzling
- 2 teaspoons balsamic vinegar
- 1½ teaspoons sea salt
- 1 teaspoon onion powder
- ½ teaspoon garlic powder
- ½ teaspoon ground sage
- ¼ teaspoon nutmeg
- freshly ground black pepper
- 1½ cups unsweetened almond milk
- 6 ounces grated sharp cheddar cheese, about 2½ cups
- 6 ounces grated gruyere cheese, about 2½ cups
- 1½ ounces finely grated pecorino cheese, ½ cup
- ¾ cup panko breadcrumbs
- 1½ teaspoons extra-virgin olive oil
Instructions
- Preheat the oven to 425°F, line a baking sheet with parchment paper, and grease a 9×13-inch baking dish.
- Slice the butternut squash in half lengthwise, scoop out the seeds, drizzle with olive oil, and sprinkle with salt and pepper. Place cut side down on the baking sheet. Wrap shallots with olive oil and salt in foil, place on the baking sheet, and roast for 30 to 45 minutes until the squash is soft.
- In a small bowl, combine panko breadcrumbs with olive oil to create the topping.
- Bring a large pot of salted water to a boil, cook the shell pasta until al dente, then reserve 1½ cups of the pasta water before draining.
- Measure 2 cups of the cooked squash flesh and blend it with the reserved pasta water, roasted shallots, olive oil, balsamic vinegar, salt, onion powder, garlic powder, sage, nutmeg, and pepper until smooth.
- Heat almond milk in the pasta pot, stir in the blended squash sauce, and cook for 3 minutes. Gradually add cheddar, Gruyere, and pecorino cheese, whisking until melted and creamy. Stir in the pasta until well-coated.
- Transfer the mixture to the baking dish, top with the panko, and broil for 5 to 10 minutes until the topping is crisp and browned.
- Allow to stand for 15 minutes before serving.
Notes
For an extra zing, you can sprinkle some fresh herbs on top before serving.
Feel free to mix in some cooked vegetables or proteins to enhance the dish.
Store leftovers in an airtight container in the fridge for up to 3 days.
Nutrition
- Serving Size: 1 serving
- Calories: 480
- Sugar: 6g
- Sodium: 900mg
- Fat: 25g
- Saturated Fat: 8g
- Unsaturated Fat: N/A
- Trans Fat: 0g
- Carbohydrates: 54g
- Fiber: 5g
- Protein: 18g
- Cholesterol: 50mg
