Cheesy Baked Butternut Squash Mac and Cheese
Cheesy Baked Butternut Squash Mac and Cheese is not your everyday comfort food. This recipe combines the creamy, luscious flavors of cheese with the subtle sweetness of roasted butternut squash, creating a dish that’s rich and nourishing. The moment you take a bite, the combination of soft pasta enveloped in a velvety cheese sauce brings a warmth that’s both satisfying and heartwarming. Not only does it feed your hunger, but it also comforts the soul.
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I first made this cheesy baked goodness on a chilly autumn evening. Honestly, it was one of those days when a big bowl of mac and cheese just felt like a hug on a plate. As the golden butternut squash roasted in the oven, filling my kitchen with its delicious aroma, I knew I had something special brewing. It’s a meal that effortlessly adapts to various occasions, from cozy family dinners to festive gatherings with friends. Trust me, once you try this Cheesy Baked Butternut Squash Mac and Cheese, you’ll find yourself making it again and again!
Why You’ll Love This Recipe
- Simple & Quick: With just 20 minutes of prep time and a hands-off baking process, this dish fits perfectly into your busy schedule.
- Irresistible Flavor: The combination of sharp cheddar and nutty Gruyere melds into a creamy sauce that’s simply divine.
- Eye-Catching Appeal: Vibrant orange squash and golden crust make this dish not only tasty but stunning on any table.
- Flexible Serving: Whether it’s a weeknight meal, a potluck, or a special occasion, this mac and cheese shines on every occasion.
- Diet-Friendly Options: With plant-based ingredients, this recipe can cater to various dietary preferences.

Ingredients You’ll Need
- 1 large butternut squash: This sweet and nutty squash forms the creamy base of the cheese sauce, providing flavor and a lovely orange hue. You can substitute it with any winter squash if needed.
- 2 shallots, roughly chopped (⅔ cup): Shallots add a delightful, mild onion flavor. Onions are a good alternative if you don’t have shallots on hand.
- 1 pound shell pasta: Shells trap the cheesy sauce perfectly, but you could use elbow macaroni or pipe rigate too.
- ¼ cup extra-virgin olive oil: Adds richness and helps roast the squash. Feel free to use another light oil, or butter, if preferred.
- 2 teaspoons balsamic vinegar: Offers a subtle tang that enhances the sweetness of the squash.
- 1½ teaspoons sea salt: Enhances all the flavors in this dish, bringing them forward.
- 1 teaspoon onion powder: For an extra layer of onion flavor.
- ½ teaspoon garlic powder: Adds a touch of warmth and depth.
- ½ teaspoon ground sage: Complements butternut squash beautifully; thyme could be swapped if you want a different herb.
- ¼ teaspoon nutmeg: Just a pinch of nutmeg rounds out the flavor, adding that wonderful warmth.
- Freshly ground black pepper: To taste; it adds a delightful spice.
- 1½ cups unsweetened almond milk: Keeps the dish creamy and vegan-friendly. Regular milk works just as well if you prefer.
- 6 ounces grated sharp cheddar cheese (about 2½ cups): This gives the dish its deliciously cheesy base.
- 6 ounces grated Gruyere cheese (about 2½ cups): Adds a nutty flavor and creamy texture. Swiss cheese can be used as a substitute.
- 1½ ounces finely grated pecorino cheese (½ cup): Provides a salty kick that enhances both flavor and depth.
- ¾ cup panko breadcrumbs: The topping adds a delightful crunch; for gluten-free diets, use gluten-free panko.
- 1½ teaspoons extra-virgin olive oil: To mix with panko for that perfect crispy topping.
How to Make Cheesy Baked Butternut Squash Mac and Cheese
Preheat the Oven: Preheat your oven to 425°F. This ensures that your squash roasts beautifully and develops a sweet flavor. Line a baking sheet with parchment paper and grease a 9×13-inch baking dish to prevent sticking.
Prepare the Squash: Slice the butternut squash in half lengthwise and scoop out the seeds. Drizzle the cut sides with 2 teaspoons of olive oil, and sprinkle with ½ teaspoon of sea salt and freshly ground black pepper. Place them cut side down on the prepared baking sheet. For the shallots, wrap them in a piece of foil after drizzling them with olive oil and adding a sprinkle of salt. Place both the squash and foil-wrapped shallots in the oven and roast for 30 to 45 minutes, or until the squash is tender and easily pierced with a fork.
Make the Topping: While your squash is roasting, prepare the topping by placing ¾ cup of panko breadcrumbs in a small bowl. Drizzle with 1½ teaspoons of olive oil and toss to combine. This step will give your Mac and Cheese that perfect crunchy contrast.
Cook the Pasta: Bring a large pot of salted water to a boil and cook 1 pound of shell pasta according to the package instructions until al dente. Remember to reserve 1½ cups of starchy pasta water before draining. This pasta water will help thin out the sauce later and aid in creating a creamy consistency.
Blend the Sauce: Once the squash is roasted and cooled slightly, measure out 2 cups of the cooked squash flesh and transfer it to a blender. Add the reserved starchy pasta water, the roasted shallots, ¼ cup of olive oil, 2 teaspoons of balsamic vinegar, 1½ teaspoons of salt, 1 teaspoon onion powder, ½ teaspoon garlic powder, ½ teaspoon ground sage, ¼ teaspoon nutmeg, and several grinds of black pepper. Blend everything until it’s silky and creamy.
Heat the Sauce: Return the pasta pot to the stove and warm 1½ cups of unsweetened almond milk over medium heat. Stir in the blended squash mixture, cooking for about 3 minutes while stirring frequently until warmed through.
Add the Cheese: Gradually whisk in 6 ounces of grated sharp cheddar cheese, 6 ounces of grated Gruyere cheese, and 1½ ounces of finely grated pecorino cheese. Make sure each cheese melts completely before adding the next for a perfectly creamy sauce.
Combine with Pasta: Once all the cheese is melted, add the drained pasta to the sauce. Stir gently until every shell is coated in the rich, cheesy mixture.
Broil for Crunch: Preheat your oven broiler, then pour the pasta and cheese mix into your greased baking dish. Sprinkle the crunchy panko on top and broil for 5 to 10 minutes, or until the topping is golden and crisp. Keep an eye on it so it doesn’t burn—perfection comes with vigilance!
Let Stand: Allow the Cheesy Baked Butternut Squash Mac and Cheese to sit for about 15 minutes before serving. This will give the dish time to set slightly, making it easier to serve.

Storing & Reheating
To store any leftovers, let the Cheesy Baked Butternut Squash Mac and Cheese cool to room temperature, then cover tightly and refrigerate in an airtight container for up to 3 days. If you want to freeze it, place it in a freezer-safe container, ensuring an airtight seal, and enjoy it within 3 months. When reheat, pop it in the oven at 350°F for about 20 minutes, or until heated through, keeping in mind the texture may be a little different from when it was first made. To refresh the dish, you can add a splash of almond milk to bring back that creamy consistency.
Chef’s Helpful Tips
- Be careful not to overcook the pasta; it should be slightly firm or al dente, as it will continue to cook in the oven.
- For a richer flavor, consider using a mix of sharp and mild cheeses, or even adding some blue cheese for a gourmet twist.
- If you find your sauce too thick, simply stir in a little more almond milk or reserved pasta water until you reach the desired consistency.
- Make the sauce and cook the pasta ahead of time, then combine just before broiling for a quick weeknight dinner.
- Don’t skip the resting time after broiling—this will help the dish firm up, making serving easier!
Cheesy Baked Butternut Squash Mac and Cheese embodies comfort and flavor in every bite. It’s versatile enough to be enjoyed on its own or as a side, plus, it’s a great way to sneak in some veggies! So, gather your ingredients and indulge in this cheesy delight. You won’t regret adding this creamy, dreamy dish to your recipe repertoire!
Recipe FAQs
Can I make this dish vegan?
Absolutely! You can substitute the cheeses with vegan alternatives and use your favorite plant-based milk. The panko topping can also be made vegan by ensuring all ingredients are dairy-free.
Can I use other types of pasta?
Yes! While shell pasta is fantastic for trapping the cheese sauce, you can use elbow macaroni, penne, or any pasta you have on hand. Just adjust the cooking time accordingly.
How can I make this dish gluten-free?
You can replace the regular pasta with gluten-free pasta and use gluten-free panko breadcrumbs for the topping. The rest of the recipe remains the same!
What can I do if my cheese sauce is too thick?
If your cheese sauce turns out thicker than you’d like, simply add a splash of reserved pasta water or almond milk until you achieve the desired creamy consistency. Stir well to combine!
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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 rich flavors into a comforting dish perfect for family dinners. It’s simple to make and features creamy cheddar, Gruyere, and nutty squash for a delightful twist on a classic favorite.
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 squash in half lengthwise and scoop out the seeds. Drizzle the cut sides with olive oil, sprinkle with salt and pepper, and place cut side down on the baking sheet. On a piece of foil, place the shallots, drizzle with olive oil, and wrap tightly. Roast for 30 to 45 minutes until the squash is soft.
- In a small bowl, toss the panko with olive oil to combine for the topping.
- Bring a large pot of salted water to a boil, and cook the pasta according to the package instructions until al dente. Reserve 1½ cups of the starchy pasta water before draining.
- Scoop 2 cups of the soft squash flesh into a blender. Add the reserved pasta water, shallots, olive oil, balsamic vinegar, salt, onion powder, garlic powder, sage, nutmeg, and several grinds of pepper. Blend until creamy.
- In the pasta pot, heat the almond milk over medium heat. Stir in the squash sauce, cooking for 3 minutes until warmed. Gradually whisk in the cheddar, Gruyere, and pecorino cheeses, melting each addition fully before adding the next. Stir in the pasta until well coated.
- Transfer the pasta to the prepared baking dish. Top with the panko and broil for 5 to 10 minutes until topping is crisp and browned.
- Let stand for 15 minutes before serving.
Notes
For a more decadent flavor, use a mix of cheeses as suggested in the ingredients.
Cooking times may vary, so check the squash for tenderness during roasting.
You can use gluten-free pasta if desired.
Nutrition
- Serving Size: 1 serving
- Calories: 550
- Sugar: 4g
- Sodium: 860mg
- Fat: 21g
- Saturated Fat: 6g
- Unsaturated Fat: 14g
- Trans Fat: 0g
- Carbohydrates: 72g
- Fiber: 5g
- Protein: 18g
- Cholesterol: 30mg
