Cheesy Baked Butternut Squash Mac and Cheese
Cheesy Baked Butternut Squash Mac and Cheese is an absolute game-changer for your comfort food repertoire. This dish combines the creamy, velvety texture of classic mac and cheese with the earthy sweetness of roasted butternut squash, creating a delightful harmony that makes every bite a joy to experience. The combination of sharp cheddar, nutty Gruyere, and salty pecorino adds depth and richness, making this mac and cheese not just a side dish but the star of the show.
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I first stumbled upon this gem during a chilly fall evening while searching for a way to bring some warmth and comfort into my home. It’s not just the melt-in-your-mouth goodness that caught my attention; it was also the vibrant, golden color of the squash that drew me in. What I love about this recipe is that it’s easy to whip up, budget-friendly, and perfect for gatherings with friends and family. Plus, it’s a fantastic way to sneak in some extra veggies, making it a hit with both kids and adults. I can’t wait for you to try it—you’re in for a delicious treat!
Why You’ll Love This Recipe
- Simple & Quick: With just 20 minutes of prep and 80 minutes of cooking, you’ll have a hearty meal ready in no time.
- Irresistible Flavor: The blend of cheeses paired with sweet, roasted butternut squash creates a rich, satisfying dish that’s packed with flavor.
- Eye-Catching Appeal: The beautiful golden hue and crispy top make it a showstopper on any dinner table.
- Flexible Serving: Perfect as a cozy dinner, a side dish for holiday gatherings, or even a comforting lunch throughout the week.
- Diet-Friendly Options: Easily adjustable for vegan or gluten-free diets with a few simple swaps.

Ingredients You’ll Need
- 1 large butternut squash: This provides the creamy base for the sauce, adding both texture and a subtly sweet taste. Look for a squash that feels heavy for its size and has a smooth, firm skin.
- 2 shallots, roughly chopped (⅔ cup): Shallots add a mild onion flavor without being overpowering. You can substitute with yellow onions if needed.
- 1 pound shell pasta (or pipe rigate or elbows): Use your favorite type of pasta. Shells hold on to the sauce beautifully, but any shape you enjoy will work.
- ¼ cup extra-virgin olive oil, plus more for drizzling: This healthy fat helps to enhance the flavors. If you are looking to switch things up, avocado oil also works.
- 2 teaspoons balsamic vinegar: A touch of acidity balances the richness of the cheese and squash. Red wine vinegar can be a suitable alternative if necessary.
- 1½ teaspoons sea salt: Essential for seasoning. You can adjust the amount based on dietary needs.
- 1 teaspoon onion powder: Adds an extra layer of onion flavor that complements the shallots.
- ½ teaspoon garlic powder: Enhances the overall taste, giving it that delightful umami hit.
- ½ teaspoon ground sage: Its earthy flavor pairs wonderfully with squash. You can swap it with dried thyme for a slight variation.
- ¼ teaspoon nutmeg: A pinch of nutmeg brightens the whole dish, making it feel more comforting. Freshly grated is best but ground works just fine.
- Freshly ground black pepper: This gives a little kick and depth to the overall flavor.
- 1½ cups unsweetened almond milk: Provides creaminess without dairy. Feel free to use any kind of plant-based milk or whole milk if preferred.
- 6 ounces grated sharp cheddar cheese (about 2½ cups): Adds a tangy flavor that accentuates the creaminess. For a milder taste, you can use medium cheddar.
- 6 ounces grated Gruyere cheese (about 2½ cups): Offers a slightly nutty and complex flavor. Substitute with Emmental if needed.
- 1½ ounces finely grated pecorino cheese (½ cup): This salty cheese adds richness. You can replace it with Parmesan if you want.
- ¾ cup panko breadcrumbs: These create a crunchy topping. If you need a gluten-free option, check for gluten-free breadcrumbs or crushed cornflakes.
- 1½ teaspoons extra-virgin olive oil: Used to mix with the panko for a crispy, golden topping.
How to Make Cheesy Baked Butternut Squash Mac and Cheese
Preheat the oven: Start by preheating your oven to 425°F. This high temperature will ensure your butternut squash gets nicely roasted. Line a baking sheet with parchment paper for easy cleanup and grease a 9×13-inch baking dish to keep everything from sticking.
Roast the squash and shallots: Carefully slice the butternut squash in half lengthwise and scoop out the seeds with a spoon. 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 prepared baking sheet. Next, wrap the chopped shallots in a piece of aluminum foil, drizzle with olive oil and sprinkle a bit of salt before sealing it tightly. Place the wrapped shallots on the baking sheet. Roast everything for 30 to 45 minutes or until the squash is very soft when pierced with a fork.
Prepare the topping: While the squash and shallots roast, combine the panko breadcrumbs with 1½ teaspoons of extra-virgin olive oil in a small bowl. Toss to ensure all the breadcrumbs are coated, which will help them crisp up nicely during baking.
Boil the pasta: In a large pot, bring salted water to a rolling boil. Cook 1 pound of shell pasta according to the package instructions, stirring until al dente, about 8 to 10 minutes. Remember to reserve 1½ cups of the starchy pasta water before draining, as you’ll use it later for the sauce.
Blend the squash mixture: Measure out 2 cups of the cooked, soft squash flesh and transfer it to a blender along with the reserved pasta water, the roasted shallots, ¼ cup extra-virgin 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 a few grinds of black pepper. Blend until completely creamy and smooth.
Combine the sauce and pasta: Place the same pot back on the stove over medium heat and pour in 1½ cups of unsweetened almond milk. Stir in the blended squash sauce and cook, stirring frequently, for about 3 minutes or until warmed through. Gradually whisk in the grated sharp cheddar, Gruyere, and pecorino cheeses. Make sure each addition is fully melted before adding more. Once all the cheese is melted and the sauce is perfectly creamy, fold in the cooked pasta until thoroughly coated.
Broil the mac and cheese: Now that you have your luscious sauce and pasta mixed together, transfer the entire mixture into your greased 9×13-inch baking dish. Sprinkle the panko mixture evenly over the top. Preheat the oven broiler and place the dish under it for 5 to 10 minutes, or until the topping is crisp and golden brown. Keep an eye on it to prevent burning!
Cool before serving: Allow the Cheesy Baked Butternut Squash Mac and Cheese to stand for about 15 minutes before digging in. This rest period helps the flavors meld beautifully and makes serving easier.

Storing & Reheating
If you happen to have leftovers, you can store Cheesy Baked Butternut Squash Mac and Cheese at room temperature for up to 2 hours after cooking. For longer storage, refrigerate in an airtight container for about 3 to 5 days. You can also freeze it for up to 3 months. When reheating, place in the oven at 350°F for about 20 minutes or until heated through, adding a splash of almond milk if needed to revive the creamy texture.
Chef’s Helpful Tips
- Avoid overcooking the pasta: Since it’s going to bake in the oven, cooking it until just al dente prevents it from getting mushy.
- Adjust the cheese: Feel free to mix and match other cheeses like Fontina or mozzarella for different flavors!
- Don’t skip the resting time: Giving the dish a 15-minute rest allows the sauce to thicken, making it easier to serve.
- Tweak the spices: If you love a bit of heat, add a dash of cayenne pepper or red pepper flakes to the squash mixture for a kick.
- Make-ahead option: Assemble the dish ahead of time and store it in the fridge. Just broil it before serving.
If you’re seeking a warm, cheesy hug in a dish, this recipe is a wonderful choice. The creamy butternut squash sauce transforms a classic staple into something new and exciting. Don’t hesitate to play around with the ingredients to fit your palate—whether it’s a cheese swap or adding a pinch of your favorite herbs. Enjoy every delicious spoonful and watch as this dish becomes a new favorite at your table!
Recipe FAQs
Can I make this dish vegan?
Absolutely! To make Cheesy Baked Butternut Squash Mac and Cheese vegan, substitute the cheese with your favorite plant-based cheese options and replace the almond milk with a creamy coconut or soy milk. Just make sure the breadcrumbs are also vegan-friendly.
How do I store leftovers?
After allowing the dish to cool down, store any leftovers in an airtight container in the fridge for up to 3 to 5 days. You can also freeze it for up to 3 months in a freezer-safe container. Just make sure to label it with the date!
Can I use a different type of pasta?
Of course! Feel free to use any pasta shape you prefer, such as penne, elbows, or fusilli. Just keep an eye on cooking times, as different shapes may vary slightly.
How do I prevent the topping from burning while broiling?
To prevent the topping from burning, keep a close watch while broiling and rotate the baking dish halfway through for even cooking. If the top starts to brown too quickly, you can cover it loosely with foil for the last few minutes of cooking.
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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 blends the sweet flavors of roasted butternut squash with creamy cheeses and crunchy panko, making it a perfect comfort food for quick dinners or gatherings. Easy to prepare and full of flavor!
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 in foil, drizzle with olive oil, sprinkle with salt, and place on the baking sheet. Roast for 30 to 45 minutes until soft.
- For the topping, combine panko and olive oil in a small bowl and toss.
- Bring a large pot of salted water to a boil. Cook the pasta according to package instructions until al dente. Reserve 1½ cups of the starchy pasta water before draining.
- In a blender, combine 2 cups of the cooked squash flesh, reserved pasta water, shallots, olive oil, balsamic vinegar, sea salt, onion powder, garlic powder, sage, nutmeg, and several grinds of pepper. Blend until creamy.
- In the pan, heat almond milk over medium. Stir in the squash sauce and cook for 3 minutes, stirring often. Gradually add cheddar, Gruyere, and pecorino cheeses, whisking until fully melted and creamy. Add the pasta and stir to coat.
- Preheat the oven broiler. Transfer pasta to the prepared baking dish, top with panko, and broil for 5 to 10 minutes until topping is crisp and browned.
- Let stand for 15 minutes before serving.
Notes
Feel free to mix the cheeses according to your preference.
For extra flavor, you can add cooked bacon or sage leaves during baking.
Nutrition
- Serving Size: 1 serving
- Calories: 540
- Sugar: 5g
- Sodium: 900mg
- Fat: 24g
- Saturated Fat: 7g
- Unsaturated Fat: 17g
- Trans Fat: 0g
- Carbohydrates: 66g
- Fiber: 4g
- Protein: 18g
- Cholesterol: 30mg
