Cheesy Baked Butternut Squash Mac and Cheese
Cheesy Baked Butternut Squash Mac and Cheese is truly a comfort food like no other. The creamy texture melds beautifully with the sharpness of cheese, creating a velvety sauce that envelops the pasta in its warm embrace. The addition of roasted butternut squash provides a subtle sweetness, making each bite a harmonious balance of flavors. The crispy panko topping adds an irresistible crunch that elevates this dish to new heights. Whether you’re looking for a cozy weeknight dinner or a dish to impress friends at a gathering, this recipe is sure to steal the show.
Table of Contents

I first stumbled upon this delightful creation during a chilly autumn evening when I craved something warm and filling. The idea of a classic mac and cheese, enhanced by the wholesome goodness of butternut squash, intrigued me. With just the right amount of cheese, and a hint of nutmeg, this dish quickly became a family favorite. The beauty of Cheesy Baked Butternut Squash Mac and Cheese lies in its simplicity—it’s easy to whip up with pantry staples while still being impressive enough to serve at dinner parties. I’m excited to share this recipe with you and hope it warms your heart and tummy just as it does mine.
Why You’ll Love This Recipe
- Simple & Quick: Ready in about 90 minutes with just 20 minutes of prep—perfect for a busy weeknight!
- Irresistible Flavor: Creamy, cheesy goodness paired with the naturally sweet taste of roasted butternut squash.
- Eye-Catching Appeal: A beautiful golden crust that’s both inviting and impressive when served.
- Flexible Serving: Ideal for cozy family dinners, potlucks, or even as a filling lunch prep.
- Diet-Friendly Options: Easily adaptable for gluten-free (using gluten-free pasta) or vegan diets (swap with plant-based cheeses).

Ingredients You’ll Need
- 1 large butternut squash: The star of the dish, it adds creaminess and a natural sweetness. Choose one that feels heavy and has a firm skin.
- 2 shallots, roughly chopped (⅔ cup): These add a lovely mild onion flavor; onions can be used as an alternative if needed.
- 1 pound shell pasta, or pipe rigate or elbows: These shapes hold onto the sauce beautifully. Feel free to use any pasta shape you prefer.
- ¼ cup extra-virgin olive oil, plus more for drizzling: Enhances the roasted flavor; avocado oil works in a pinch.
- 2 teaspoons balsamic vinegar: A touch of acidity to balance the richness of the cheese; red wine vinegar is a substitute.
- 1½ teaspoons sea salt: Essential for flavoring the dish; adjust to taste based on dietary needs.
- 1 teaspoon onion powder: Adds depth to the sauce; fresh onions can substitute if using more shallots.
- ½ teaspoon garlic powder: Gives a subtle garlicky aroma; fresh minced garlic also works well.
- ½ teaspoon ground sage: This herb pairs wonderfully with butternut squash; thyme can be a delicious alternative.
- ¼ teaspoon nutmeg: A pinch adds warmth; this is optional but recommended for a lovely spice note.
- Freshly ground black pepper: Adds flavor and a bit of heat; adjust to your preference.
- 1½ cups unsweetened almond milk: Keeps the dish dairy-free in a creamy manner; use regular milk or any plant-based milk as an alternative.
- 6 ounces grated sharp cheddar cheese (about 2½ cups): Offers great flavor; feel free to use mild cheddar or a vegan cheese option.
- 6 ounces grated gruyere cheese (about 2½ cups): Adds a nutty creaminess; Swiss cheese is a good substitute.
- 1½ ounces finely grated pecorino cheese (½ cup): For finishing touches that elevate the dish; parmesan is a great alternative.
- ¾ cup panko breadcrumbs: Provides a delightful crunch on top; regular breadcrumbs can be used, but panko gives a lighter texture.
- 1½ teaspoons extra-virgin olive oil: Ensures the panko browns nicely; butter can substitute for added richness.
How to Make Cheesy Baked Butternut Squash Mac and Cheese
Preheat the oven: Preheat your oven to 425°F (220°C). Line a baking sheet with parchment paper and grease a 9×13-inch baking dish to get ready for the layers of deliciousness to come.
Prepare the butternut squash and shallots: Slice the butternut squash in half lengthwise and scoop out the seeds. Drizzle the cut sides with 1 tablespoon of olive oil and sprinkle with sea salt and freshly ground black pepper. Place cut-side down on the baking sheet. Wrap the chopped shallots in foil, drizzle with more olive oil, sprinkle with salt, and seal tightly. Place it on the baking sheet and roast for 30 to 45 minutes, or until the squash is soft.
Make the topping: While your squash and shallots are roasting, grab a small bowl and combine the ¾ cup of panko breadcrumbs with 1½ teaspoons of olive oil. Toss them gently until the crumbs are coated and set aside for that beautiful topping.
Cook the pasta: Bring a large pot of salted water to a boil. Add the 1 pound of shell pasta and cook according to the package instructions until al dente. Remember to reserve 1½ cups of the starchy pasta water before draining!
Blend the sauce: Scoop 2 cups of the cooked, soft squash flesh into a blender. Add the reserved 1½ cups of pasta water, roasted shallots, 2 tablespoons of olive oil, 2 teaspoons of balsamic vinegar, 1½ teaspoons of sea salt, 1 teaspoon of onion powder, ½ teaspoon of garlic powder, ½ teaspoon of ground sage, ¼ teaspoon of nutmeg, and several grinds of black pepper. Blend until the mixture is creamy and smooth.
Combine the pasta and sauce: Place the empty pasta pot back on the stove over medium heat, pouring in 1½ cups of unsweetened almond milk. Stir in the squash sauce and heat, stirring often, for about 3 minutes or until warmed through. Gradually whisk in the 6 ounces of grated sharp cheddar cheese, then the 6 ounces of grated Gruyere cheese, followed by the 1½ ounces of finely grated pecorino cheese, ensuring each addition is fully melted before adding the next. Once the sauce is creamy, add the drained pasta and stir until all is beautifully combined.
Broil the mac and cheese: Preheat your oven’s broiler. Gently transfer the pasta mixture to your prepared baking dish. Top it generously with the prepared panko breadcrumbs and place it under the broiler for 5 to 10 minutes, watching closely, until the topping is crisp and golden brown.
Cool and serve: Allow the baking dish to sit for 15 minutes before serving. This lets the flavors meld beautifully and makes it easier to scoop.

Storing & Reheating
Leftover Cheesy Baked Butternut Squash Mac and Cheese can be stored at room temperature for up to 2 hours after serving. After that, transfer it to an airtight container and store it in the refrigerator for up to 3 days. For longer storage, you can freeze it in a freezer-safe container for up to 3 months. When you’re ready to enjoy it again, simply reheat in the oven at 350°F (175°C) for about 20 minutes, or until warmed through. Keep in mind that the texture may change slightly, but you can refresh it by adding a splash of almond milk before reheating.
Chef’s Helpful Tips
- Avoid overcooking the pasta; you want it al dente since it will continue to cook in the oven!
- If you prefer a creamier sauce, feel free to add a bit more almond milk when combining the pasta and sauce.
- Taste and adjust the seasoning! Every squash can vary in sweetness, so you might need a pinch more salt or a dash of vinegar for balance.
- If preparing ahead of time, you can make the sauce and pasta separately, then combine and bake just before serving for a fresh dish.
This dish not only showcases the delightful flavors of fall but also brings comfort and fulfillment to your table. With an easy-to-follow recipe that yields a generous 8 servings, it’s perfect for gatherings or simply enjoying at home. Don’t shy away from experimenting with additional spices or cheese variations to make it your own! Whether it’s a cozy weeknight or a cheerful weekend reunion, Cheesy Baked Butternut Squash Mac and Cheese is bound to be a hit. Join me in the kitchen, and let’s share in the joy of cooking and good food.
Recipe FAQs
Can I use a different type of cheese?
Absolutely! While sharp cheddar and Gruyere give this dish a great flavor, feel free to experiment with cheeses like mozzarella, fontina, or even a spicy pepper jack for a twist. Just keep the ratios about the same to maintain creamy texture.
Is this recipe suitable for meal prep?
Yes, this mac and cheese is fantastic for meal prep! You can prepare it ahead of time, then store it in the refrigerator for up to 3 days, or freeze it for later. Just ensure it’s cooled completely before sealing.
Can I make this dish gluten-free?
Certainly! You can substitute the shell pasta with a gluten-free pasta option and ensure that all other ingredients, including the panko breadcrumbs, are certified gluten-free. The end result will still be an incredible dish!
How can I add more vegetables?
Adding sautéed spinach, kale, or roasted Brussels sprouts can enhance the nutrient profile of this dish. Just stir them into the pasta before baking, or mix them into the sauce for a delightful veggie twist!
PrintMore Dinner Recipes
- Burger Bowls with Chipotle Ranch Sweet Potato Fries
- Healthy Steak Avocado Corn Bowl
- Oven Baked Chicken Cutlets
- Cajun Shrimp and Sausage Pasta
- Crockpot Teriyaki Steak Bites
Did You Enjoy Making This Recipe? Please rate this recipe with ⭐⭐⭐⭐⭐ or leave a comment.
📖 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: Dinner
- Method: Baking
- Cuisine: American
Description
This Cheesy Baked Butternut Squash Mac and Cheese offers a delightful blend of flavors that makes it a perfect comfort food. With its creamy texture and savory taste from sharp cheddar and Gruyere cheese, it stands as an ideal choice for a satisfying dinner or a warm family gathering. Simple to prepare yet rich in flavor, this dish is just the kind of homemade comfort food you need.
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 with olive oil and salt, and add to the baking sheet. Roast for 30-45 minutes until the squash is soft.
- In a small bowl, combine panko breadcrumbs with olive oil for the topping.
- Boil salted water in a large pot, cook the pasta according to package instructions until al dente, reserving 1½ cups of pasta water before draining.
- Transfer 2 cups of cooked squash into a blender with reserved pasta water, shallots, olive oil, balsamic vinegar, salt, onion powder, garlic powder, sage, nutmeg, and pepper. Blend until smooth and creamy.
- Return pasta pot to stove, warm almond milk over medium heat, add blended squash mixture, and cook for 3 minutes. Gradually whisk in cheddar, Gruyere, and pecorino until melted and creamy, then add pasta and stir until coated.
- Broil the pasta in the baking dish topped with panko for 5-10 minutes until golden and crisp.
- Allow to cool for 15 minutes before serving.
Notes
You can substitute the pasta type according to your preference; just ensure to adjust cooking time as needed.
For extra flavor, try adding cooked vegetables or spices to the cheese sauce before mixing in the pasta.
Nutrition
- Serving Size: 1 serving
- Calories: 410
- Sugar: 3g
- Sodium: 770mg
- Fat: 17g
- Saturated Fat: 6g
- Carbohydrates: 56g
- Fiber: 3g
- Protein: 14g
- Cholesterol: 30mg





