Pin it
Blending roasted butternut squash into the cheese sauce creates mac and cheese that's creamier than the traditional flour-based version while sneaking in vegetables. The squash adds subtle sweetness and velvety texture that makes the cheese sauce incredibly smooth, and roasting it first with shallots builds deeper flavor than using raw squash. Three different cheeses - Gruyere, sharp cheddar, and pecorino - melt together into something rich and complex. A crispy panko topping adds textural contrast, and the whole thing feels like peak fall comfort food that happens to be more nutritious than regular mac and cheese.
Butternut squash mac and cheese started as an attempt to recreate the Trader Joe's frozen version at home. Learning that roasted squash could replace the traditional flour roux was revolutionary because it creates even creamier texture while adding nutrition. My first attempt used raw squash that I just steamed, which tasted bland and watery. Roasting the squash and shallots together until caramelized made all the difference by concentrating flavors and sweetness. Now I roast extra squash whenever I'm using my oven and freeze it specifically for making this mac and cheese quickly on busy weeknights.
Ingredients and Why They Matter
- Butternut squash (1 large, about 3 pounds): Roasted until soft and sweet; need 2 cups for the sauce
- Shallots (2 medium): Roasted alongside squash to add mild onion flavor
- Pasta shells (1 pound): Shape that holds sauce well; elbow macaroni or rigatoni substitute
- Gruyere cheese (6 ounces, grated): Nutty, slightly sweet cheese that melts beautifully
- Sharp cheddar cheese (6 ounces, grated): Tangy, classic mac and cheese flavor
- Pecorino or parmesan (2 ounces, grated): Salty, savory depth
- Unsweetened almond milk (1½ cups): Base for cheese sauce; whole milk or 2% substitute
- Reserved pasta water (1½ cups): Starchy liquid that helps blend the squash and thin the sauce
- Extra virgin olive oil (3 tablespoons, divided): For roasting and blending
- Balsamic vinegar (1 tablespoon): Adds tangy brightness that balances sweetness
- Ground sage (½ teaspoon): Earthy fall flavor
- Ground nutmeg (¼ teaspoon): Warm spice that enhances squash
- Garlic powder (½ teaspoon): Savory depth
- Onion powder (½ teaspoon): Umami boost
- Panko breadcrumbs (¾ cup): Creates crispy topping
- Salt and black pepper (to taste): Essential seasoning
How To Make It
- Roast the squash and shallots:
- Preheat your oven to 425°F. Cut the butternut squash in half lengthwise and scoop out all the seeds with a spoon. Peel the shallots and cut them in half. Place the squash halves cut-side up on a rimmed baking sheet along with the shallot halves. Drizzle with 1 tablespoon olive oil and season generously with salt and pepper. Roast for 45-55 minutes until the squash flesh is completely soft and caramelized around the edges - a fork should slide through with no resistance. Let cool slightly, then scoop out the soft squash flesh. You need 2 cups of roasted squash. This step can be done up to 4 days ahead - just store the cooled squash and shallots in an airtight container in the refrigerator, or freeze for up to 3 months.
- Cook the pasta:
- While the squash roasts (or when ready to proceed if you roasted ahead), bring a large pot of salted water to a boil. Add the pasta shells and cook according to package directions until al dente. Before draining, use a measuring cup to scoop out and reserve 1½ cups of the starchy pasta cooking water - this is crucial for blending the sauce. Drain the pasta and set aside.
- Prepare the topping:
- In a small bowl, toss the panko breadcrumbs with 1 tablespoon olive oil and a pinch of salt until evenly coated. Set aside. This simple step ensures the topping browns evenly and becomes crispy under the broiler.
- Make the squash puree:
- Add 2 cups of the roasted butternut squash flesh, the roasted shallots, remaining 1 tablespoon olive oil, balsamic vinegar, sage, nutmeg, onion powder, garlic powder, 1 teaspoon salt, and several grinds of black pepper to a blender. Pour in the 1½ cups reserved pasta water. Blend on high speed for 1-2 minutes until completely smooth and creamy with no chunks remaining. The mixture should look like thick, smooth soup. Scrape down the sides as needed. This squash puree is the base that makes your cheese sauce incredibly creamy.
- Heat the milk:
- Return the empty pasta pot to the stove over medium heat. Pour in the almond milk and warm it for 2-3 minutes - you don't want it boiling, just warm to the touch. Pour the smooth squash puree into the warm milk and stir constantly with a whisk or wooden spoon. Cook, stirring frequently, for about 3-4 minutes until the mixture is heated through and steaming. The color should be a beautiful golden orange.
- Add the cheese:
- Reduce heat to low. Working in small handfuls at a time, add the grated Gruyere, stirring constantly with a whisk until each addition melts completely before adding the next. Repeat with the sharp cheddar, then the pecorino, whisking constantly and waiting for each addition to melt smoothly into the sauce. Don't rush this step or dump all the cheese in at once - gradual additions create silky smooth sauce instead of grainy, broken sauce. Once all the cheese is melted, the sauce should look glossy, smooth, and coat the back of a spoon. Taste and adjust seasoning with more salt and pepper if needed.
- Combine with pasta:
- Add the drained pasta to the cheese sauce. Stir gently but thoroughly to coat every piece of pasta with the luscious sauce. The pasta should look well-coated but not soupy. If the sauce seems too thick, add a splash of milk or reserved pasta water to loosen it.
- Bake with topping:
- Preheat your broiler to high. Lightly oil a 9x13-inch baking dish. Transfer the mac and cheese to the prepared dish, spreading it in an even layer. Sprinkle the oiled panko breadcrumbs evenly over the top. Place under the broiler about 6 inches from the heat source. Broil for 2-4 minutes, watching carefully, until the breadcrumbs turn golden brown and crispy. Broilers vary in intensity, so stay nearby and rotate the dish if needed for even browning. Remove from the oven and let stand for 15 minutes before serving - this allows the sauce to thicken slightly and makes serving easier. The mac and cheese will be very hot, so this resting time also prevents burnt mouths.
Pin it
Butternut squash sauce seemed weird to me before understanding it's basically just a vegetable puree used the same way you'd use a roux to thicken and enrich cheese sauce. The roasted squash provides body, creaminess, and subtle sweetness while the cheese provides all the traditional mac and cheese flavor. My kids who claim to hate squash eat this enthusiastically without realizing what's in it. The flavor reads as "extra creamy mac and cheese" rather than "squash pasta," which makes it an excellent way to increase vegetable consumption.
Cheese Selection Importance
Using three different cheeses creates more complex, interesting flavor than single-cheese versions. Gruyere provides nutty sweetness and melts into incredibly smooth sauce. Sharp cheddar delivers the tangy, familiar mac and cheese taste people expect. Pecorino or parmesan adds salty, savory depth that rounds everything out. Each cheese contributes something different. Pre-shredded cheese contains cellulose or potato starch to prevent clumping, which interferes with melting. Grating cheese yourself takes a few extra minutes but guarantees smooth, creamy results instead of grainy, separated sauce.
Roasting vs Other Cooking Methods
Roasting butternut squash concentrates its natural sugars through caramelization, creating deeper, sweeter flavor than steaming or boiling. The high heat drives off excess moisture, making the flesh denser and more flavorful. Roasting the shallots alongside adds sweet, caramelized onion notes. Steamed or boiled squash tastes bland and watery in comparison. The roasting takes longer but requires no attention - just pop it in the oven and forget it while you do other things. The intensity of flavor makes roasting worth the time investment.
Pasta Water Purpose
Starchy pasta cooking water serves multiple purposes in this recipe. The starch helps emulsify the squash puree, making it blend smoothly instead of staying grainy. The liquid thins the thick squash to sauce consistency. The mild seasoning from salted pasta water seasons the sauce throughout. Using plain water or milk alone wouldn't create the same silky texture. Always reserve pasta water before draining because you can't get it back once it's gone down the drain.
Gradual Cheese Addition
Adding cheese gradually in small portions while stirring constantly prevents the dreaded broken, grainy sauce. Cheese contains proteins and fats that need to emulsify smoothly into the liquid. Dumping all the cheese in at once overwhelms the liquid's ability to incorporate it properly, causing the fat to separate out and proteins to clump. Adding small amounts allows each addition to melt and integrate before more is added. Low heat prevents the cheese from overheating and breaking. Patience during this step determines whether your sauce is smooth and creamy or grainy and oily.
Make-Ahead and Storage
The roasted squash and shallots can be prepared up to 4 days ahead and refrigerated, or frozen for 3 months, making weeknight assembly much faster. The fully assembled mac and cheese can be refrigerated unbaked for 1 day - just add 10 minutes to the baking time if starting cold. Leftover baked mac and cheese keeps refrigerated for 3-4 days. Reheat gently in the microwave or oven at 350°F, adding a splash of milk to loosen the sauce which thickens when cold. The crispy topping will soften after storage but can be refreshed under the broiler.
Serving Suggestions
Butternut squash mac and cheese works as a main dish or side depending on the meal. Serve as a vegetarian main course with a green salad. Pair as a side with roasted chicken, pork chops, or grilled steak. Include in Thanksgiving spreads alongside turkey and traditional sides. Serve in smaller portions as an indulgent appetizer. Add roasted vegetables like broccoli or Brussels sprouts directly to the mac for a more complete meal. The rich, creamy nature means you don't need much else besides something fresh and green.
Pin it
This butternut squash mac and cheese recipe represents the kind of comfort food that satisfies cravings while sneaking in nutrition. The creamy, cheesy satisfaction of classic mac and cheese meets the subtle sweetness and nutrition of roasted squash in a combination that tastes indulgent rather than healthy. When you serve this and watch everyone go back for seconds without anyone complaining about vegetables, you know you've created something special. Sometimes the best recipes are the ones that prove healthy and delicious aren't mutually exclusive, and this mac and cheese definitely accomplishes that goal perfectly every single time you make it.
Frequently Asked Questions
- → Can I make this mac and cheese ahead of time?
- Yes! You can roast the butternut squash and shallots up to 4 days early and keep them in the fridge. Just finish assembling and baking when you're ready to eat.
- → What pasta shape works best for this recipe?
- Shell pasta, pipe rigate, or elbows all work great. Pick any shape with ridges or curves that will hold onto the creamy cheese sauce.
- → Can I use a different cheese combination?
- Sure! The cheddar, Gruyere, and pecorino combo is delicious, but you can swap in your favorite melting cheeses. Just keep the total amount around 13-14 ounces.
- → How do I know when the butternut squash is done roasting?
- The squash is ready when it feels soft and tender when you press on it. This usually takes 30 to 45 minutes at 425°F depending on the size of your squash.
- → Is this recipe gluten-free?
- Not as written, but you can easily make it gluten-free by using gluten-free pasta and gluten-free panko breadcrumbs instead of regular ones.
- → Why do I need to save the pasta water?
- The starchy pasta water helps thin out the butternut squash sauce and makes it silky smooth. It also helps the sauce stick better to the pasta.
- → Can I freeze leftover mac and cheese?
- Yes, this freezes well for up to 3 months. Let it cool completely, then store in an airtight container. Reheat in the oven at 350°F until warmed through.