
This butternut squash mac and cheese transforms the classic comfort food into a nutritious delight that's both kid-friendly and sophisticated enough for adults. The roasted squash adds a natural sweetness and velvety texture while sneaking in extra vegetables that even picky eaters won't mind.
I first made this on a chilly autumn evening when I had an abundance of butternut squash from the farmers market. My family was skeptical about "healthier" mac and cheese, but they've requested it weekly ever since that first bite.
Ingredients
- Elbow macaroni or short pasta forms the base of this dish and captures the creamy sauce in its curves and ridges [Details]
- Butternut squash provides natural sweetness, vibrant color, and velvety texture choose squash that feels heavy for its size with unblemished skin [Details]
- Olive oil helps the squash caramelize in the oven bringing out its natural sugars [Details]
- Unsalted butter gives you control over the final saltiness while adding richness [Details]
- Allpurpose flour works with butter to create a roux that thickens the sauce [Details]
- Whole milk creates the creamiest texture but can be substituted as needed [Details]
- Sharp cheddar cheese provides that classic mac and cheese flavor look for aged varieties for more depth [Details]
- Gruyère or Parmesan cheese adds complexity and umami notes [Details]
- Ground nutmeg enhances the savory qualities of the cheese and complements the sweetness of the squash [Details]
- Smoked paprika optional adds a subtle smoky dimension [Details]
- Panko breadcrumbs optional create an irresistible crunchy topping [Details]
Instructions
- Roast the Butternut Squash:
- Toss diced butternut squash with olive oil, salt, and pepper, then spread in a single layer on a parchment-lined baking tray. Roast at 200°C (400°F) for 25-30 minutes until the edges begin to caramelize and the flesh is fork-tender. The roasting process concentrates the squash's natural sweetness and adds depth to your final sauce.
- Cook the Pasta:
- While the squash roasts, bring a large pot of water to a rolling boil. Add a generous tablespoon of salt (the water should taste like seawater) before adding your pasta. Cook until just al dente, about 1-2 minutes less than package directions. The pasta will continue cooking in the sauce, so keeping it slightly firm prevents mushiness in the final dish.
- Blend the Squash:
- Transfer the roasted squash to a blender or food processor while still warm. Add 120 ml (1/2 cup) of milk and blend until completely smooth, scraping down the sides as needed. The warm squash will blend more easily than if it were cold, creating a silky base for your sauce.
- Create the Roux:
- In a large saucepan over medium heat, melt butter completely before adding flour. Whisk continuously for a full minute to cook out the raw flour taste without browning. This step is crucial for a smooth, flavorful sauce without any floury aftertaste.
- Develop the Sauce:
- Gradually pour in the remaining milk while whisking constantly to prevent lumps from forming. Continue stirring until the mixture thickens enough to coat the back of a spoon, about 2-3 minutes. The sauce should be smooth and velvety before proceeding to the next step.
- Incorporate the Cheese and Squash:
- Reduce heat to low before adding the squash puree and cheeses. Stir continuously until completely melted and incorporated. Add nutmeg and optional smoked paprika, then taste and adjust seasoning with salt and pepper. The sauce should be rich and complex with the perfect balance of cheese and squash flavors.
- Combine with Pasta:
- Add the drained pasta directly to the sauce, folding gently until each piece is thoroughly coated. If the mixture seems too thick, add a splash of the reserved pasta water to reach your desired consistency. The starch in the pasta water helps the sauce cling to the pasta.
- Add Optional Topping:
- For an irresistible textural contrast, transfer the mac and cheese to a baking dish, mix panko breadcrumbs with melted butter, and sprinkle evenly over the top. Broil for 2-3 minutes, watching carefully to avoid burning, until the top is golden and crispy.

Butternut squash is truly the star ingredient here. I discovered its magic in mac and cheese during a desperate attempt to get my children to eat more vegetables. The first time I served it, my youngest asked for seconds before I could even sit down. Now it's our special autumn tradition to pick squash together at our local farm knowing it will become this beloved dish.
Make-Ahead Options
This butternut squash mac and cheese is perfect for meal planning. You can prepare the squash puree up to three days ahead and store it in the refrigerator. When ready to use, simply warm it slightly before incorporating it into your sauce. You can also assemble the entire dish, cover it tightly, and refrigerate for up to 24 hours before baking. Just add an extra 10-15 minutes to the baking time if cooking from cold.
Flavor Variations
While this recipe is delicious as written, it's incredibly versatile. Try adding caramelized onions for sweetness, crispy sage leaves for an autumnal touch, or fold in baby spinach at the end for added nutrition. For a protein boost, stir in shredded rotisserie chicken or crispy bacon bits. Vegetarians can enjoy diced roasted mushrooms for a meaty texture without the meat. The squash base pairs beautifully with many flavors, so don't be afraid to experiment.
Kid-Friendly Adaptations
This dish is already a hit with children, but you can make it even more appealing by using fun pasta shapes like bowties, wheels, or animal shapes. If your kids are particularly skeptical about vegetables, puree the squash extra smooth and start with a smaller amount, gradually increasing it in future batches as they become accustomed to the flavor. Letting children help with safe steps like measuring ingredients or sprinkling the topping increases the likelihood they'll enjoy eating the final product.
Serving Suggestions
Serve this mac and cheese as a satisfying main course alongside a simple green salad dressed with vinaigrette to cut through the richness. For a more substantial meal, pair it with roasted Brussels sprouts or steamed broccoli. It also makes an impressive side dish for roasted chicken or grilled sausages. During holiday gatherings, this can be an unexpected but welcome addition to the traditional spread, offering a vegetarian option that doesn't sacrifice flavor or comfort.

This butternut squash mac and cheese is a crowd-pleasing dish that cleverly incorporates extra vegetables. It's a comforting yet wholesome meal perfect for families.
Recipe FAQ
- → Can I use a different type of pasta?
Yes, any short pasta like penne, shells, or fusilli works well for holding the creamy sauce.
- → How do I make this dish vegan?
Use plant-based milk, vegan butter, and your preferred dairy-free cheese for a vegan-friendly alternative.
- → What can I substitute for Gruyère?
Extra cheddar, Parmesan, or mild mozzarella are all great replacements for Gruyère if desired.
- → Can I add more vegetables?
Absolutely! Try stirring in sautéed spinach or peas for extra nutrition and color.
- → How do I make the top crispy?
Mix panko breadcrumbs with melted butter, sprinkle over the pasta, and briefly broil until golden and crisp.
- → Is this dish suitable for freezing?
For best texture, enjoy fresh. If freezing, thaw and reheat gently to maintain creaminess and avoid separation.