Cheesy Baked Butternut Squash Mac and Cheese

I used to think mac and cheese had to come from a box until I was well into my twenties. That’s just how we did it growing up. The orange powder mixed with butter and milk was comfort food at its finest.

But then I discovered you could make it from scratch with real cheese, and everything changed. Now I love experimenting with different versions, like this baked butternut squash mac and cheese that sneaks some vegetables into the mix. The squash makes it creamy and adds a bit of sweetness that pairs perfectly with the cheese. Plus, it’s a great way to get the kids to eat their veggies without them even noticing.

What Kind of Butternut Squash Should I Use?

Any medium-sized butternut squash from your grocery store will work perfectly for this recipe. Look for one that feels heavy for its size and has a smooth, tan-colored skin without any soft spots or dark blemishes. The squash should have a long neck and a bulbous bottom – the neck portion is where you’ll get most of your usable flesh since the bottom contains the seed cavity. If you’re short on time or just want to make things easier, you can absolutely use pre-cut butternut squash from the produce section, though it will cost a bit more than buying a whole squash.

Options for Substitutions

This cozy mac and cheese has room for plenty of swaps to fit what you have on hand:

• Butternut squash: Sweet potato, acorn squash, or even pumpkin puree work great here. If using canned pumpkin, you’ll need about 1 cup and can skip the roasting step entirely.
• Elbow macaroni: Any short pasta shape will do the trick – try shells, penne, or cavatappi. The key is choosing something that holds onto that creamy cheese sauce.
• Milk: Heavy cream makes it richer, while half-and-half is a nice middle ground. For dairy-free options, unsweetened oat milk or cashew milk work best for creaminess.
• Cheddar cheeses: Feel free to mix and match your favorite melting cheeses. Gruyere, fontina, or gouda all bring great flavor. Just stick with good melters and avoid pre-shredded if possible.
• Fresh rosemary: Dried rosemary works too – just use 1 teaspoon instead. Fresh thyme or sage are also nice alternatives that pair well with the squash.
• Whole wheat breadcrumbs: Regular breadcrumbs, panko, or even crushed crackers make a great crunchy topping. For extra flavor, toss them with a bit of melted butter and parmesan.

Watch Out for These Mistakes While Baking

The biggest mistake when making butternut squash mac and cheese is not roasting the squash long enough – undercooked squash will create lumps in your cheese sauce and won’t blend smoothly, so make sure it’s fork-tender before mashing or pureeing it. Another common error is adding the cheese to a sauce that’s too hot, which can cause it to seize up and become grainy instead of creamy, so let your roux cool slightly before whisking in the cheese gradually. Don’t forget to slightly undercook your pasta since it will continue cooking in the oven – aim for just shy of al dente to prevent mushy noodles in the final dish. Finally, resist the urge to skip the breadcrumb topping or add it too early, as those golden, crunchy breadcrumbs need to go on just before baking to create the perfect contrast to the creamy pasta underneath.

What to Serve With Baked Butternut Squash Mac and Cheese?

This rich and creamy mac and cheese is pretty filling on its own, but I love pairing it with something fresh and crisp to balance out all that cheesy goodness. A simple arugula salad with lemon vinaigrette cuts through the richness perfectly, or you could go with roasted Brussels sprouts or green beans for some extra veggies on the plate. If you want to make it a heartier meal, grilled chicken or pork chops work great alongside this dish. For a cozy fall dinner, I sometimes serve it with a warm spinach salad topped with dried cranberries and toasted walnuts.

Storage Instructions

Refrigerate: This butternut squash mac and cheese keeps really well in the fridge for up to 4 days in a covered dish. The flavors actually get even better after a day or two! I like to cover it tightly with foil or transfer it to an airtight container once it’s completely cooled.

Freeze: You can definitely freeze this for up to 3 months, which makes it perfect for meal prep. Let it cool completely first, then wrap it well in plastic wrap and foil, or portion it into freezer-safe containers. Just know that the texture might be slightly different after freezing, but it’s still delicious.

Reheat: To warm it back up, cover with foil and bake at 350°F for about 20-25 minutes if it’s been in the fridge, or 45-60 minutes if frozen. You can also microwave individual portions, but I like to add a splash of milk to keep it creamy and maybe sprinkle some extra cheese on top.

Estimated Nutrition

Estimated nutrition for the whole recipe (without optional ingredients):

• Calories: 1750-1900
• Protein: 55-65 g
• Fat: 65-75 g
• Carbohydrates: 220-240 g

Ingredients

For the casserole base:

• 1/2 medium butternut squash (peeled, deseeded, chopped)
• 1 tbsp olive oil
• Kosher salt, to taste
• Black pepper, as needed
• 8 oz elbow macaroni

For the sauce:

• 2 1/2 cups milk, separated
• 2 tbsp butter
• 3 tbsp all-purpose flour
• 1/8 tsp ground nutmeg
• 1 tbsp chopped fresh rosemary

For assembly and topping:

• 1 cup shredded aged white cheddar cheese
• 1 cup grated sharp cheddar cheese
• 3/4 cup whole wheat breadcrumb

Step 1: Roast the Butternut Squash

• 1/2 medium butternut squash (peeled, deseeded, chopped)
• 1 tbsp olive oil
• kosher salt, to taste
• black pepper, as needed

Preheat your oven to 400°F (200°C).

Place the peeled, deseeded, and chopped butternut squash on a large baking sheet.

Drizzle with olive oil and toss to coat.

Sprinkle with kosher salt and black pepper as desired.

Roast in the oven for 20–30 minutes, turning once halfway, until the squash is fork-tender.

Once roasting is finished, reduce the oven temperature to 350°F (175°C).

Step 2: Cook the Elbow Macaroni

• 8 oz elbow macaroni
• kosher salt, to taste (for pasta water)

While the squash is roasting, bring a pot of salted water to a boil.

Add elbow macaroni and cook according to the package instructions until al dente.

Drain well and set aside until needed.

Step 3: Make the Butternut Squash Purée

• roasted butternut squash (from Step 1)
• 1/2 cup milk (from 2 1/2 cups total)

Transfer the roasted butternut squash from Step 1 to a food processor or blender.

Blend until completely smooth.

Add in 1/2 cup of the milk and blend again to achieve a creamy, thinned purée.

I find this step helps the squash integrate seamlessly into the cheese sauce for a velvety texture.

Step 4: Make the Cheese Sauce and Combine

• 2 tbsp butter
• 3 tbsp all-purpose flour
• 1/8 tsp ground nutmeg
• 2 cups milk (remaining from 2 1/2 cups)
• butternut squash purée (from Step 3)
• 1 tbsp chopped fresh rosemary
• cooked elbow macaroni (from Step 2)
• kosher salt, to taste
• black pepper, as needed

In a large skillet over medium heat, melt the butter.

Once melted, whisk in the flour and nutmeg.

Cook, whisking constantly, for 2–3 minutes until the mixture is fragrant and just beginning to brown slightly.

Gradually add the remaining 2 cups of milk, whisking to make a smooth sauce.

Turn the heat to high and bring to a gentle boil, continuing to whisk until the sauce thickens.

Reduce the heat to low and whisk in the butternut squash purée from Step 3, followed by the chopped fresh rosemary.

Add the drained elbow macaroni from Step 2 and stir until all noodles are well coated in sauce.

Season with kosher salt and black pepper to taste.

I like to taste the sauce here and adjust the salt, or even add a pinch more nutmeg for extra warmth.

Step 5: Assemble the Casserole

• macaroni and cheese mixture (from Step 4)
• 1 cup shredded aged white cheddar cheese
• 1 cup grated sharp cheddar cheese
• 3/4 cup whole wheat breadcrumb

Grease a 2-quart casserole dish.

Spoon half of the macaroni and cheese mixture from Step 4 into the dish.

Sprinkle half of the aged white cheddar and half of the sharp cheddar cheese over the noodles.

Add the remaining macaroni mixture on top, then cover with the rest of the aged cheddar and sharp cheddar.

Sprinkle the whole wheat breadcrumbs evenly over the entire surface.

Step 6: Bake and Serve

Place the assembled casserole in the oven at 350°F (175°C) and bake for 25–30 minutes, or until the macaroni and cheese is bubbling and the breadcrumbs are golden brown.

Remove from the oven and allow it to rest for 5 minutes before serving.

For an extra touch, I sometimes broil the top for 1-2 minutes at the end for a super crispy crust.

Cheesy Baked Butternut Squash Mac and Cheese

Delicious Cheesy Baked Butternut Squash Mac and Cheese recipe with step-by-step instructions.

Print Recipe Pin Recipe

Prep Time 26 minutes mins

Cook Time 54 minutes mins

Total Time 1 hour hr 20 minutes mins

Servings 4

Calories 1825 kcal

Ingredients

  

For the casserole base:

• 1/2 medium butternut squash (peeled, deseeded, chopped)
• 1 tbsp olive oil
• kosher salt, to taste
• black pepper, as needed
• 8 oz elbow macaroni

For the sauce:

• 2 1/2 cups milk, separated
• 2 tbsp butter
• 3 tbsp all-purpose flour
• 1/8 tsp ground nutmeg
• 1 tbsp chopped fresh rosemary

For assembly and topping:

• 1 cup shredded aged white cheddar cheese
• 1 cup grated sharp cheddar cheese
• 3/4 cup whole wheat breadcrumb

Instructions

 

• Preheat your oven to 400°F (200°C). Place the peeled, deseeded, and chopped butternut squash on a large baking sheet. Drizzle with olive oil and toss to coat. Sprinkle with kosher salt and black pepper as desired. Roast in the oven for 20–30 minutes, turning once halfway, until the squash is fork-tender. Once roasting is finished, reduce the oven temperature to 350°F (175°C).
• While the squash is roasting, bring a pot of salted water to a boil. Add elbow macaroni and cook according to the package instructions until al dente. Drain well and set aside until needed.
• Transfer the roasted butternut squash from Step 1 to a food processor or blender. Blend until completely smooth. Add in 1/2 cup of the milk and blend again to achieve a creamy, thinned purée. I find this step helps the squash integrate seamlessly into the cheese sauce for a velvety texture.
• In a large skillet over medium heat, melt the butter. Once melted, whisk in the flour and nutmeg. Cook, whisking constantly, for 2–3 minutes until the mixture is fragrant and just beginning to brown slightly. Gradually add the remaining 2 cups of milk, whisking to make a smooth sauce. Turn the heat to high and bring to a gentle boil, continuing to whisk until the sauce thickens. Reduce the heat to low and whisk in the butternut squash purée from Step 3, followed by the chopped fresh rosemary. Add the drained elbow macaroni from Step 2 and stir until all noodles are well coated in sauce. Season with kosher salt and black pepper to taste. I like to taste the sauce here and adjust the salt, or even add a pinch more nutmeg for extra warmth.
• Grease a 2-quart casserole dish. Spoon half of the macaroni and cheese mixture from Step 4 into the dish. Sprinkle half of the aged white cheddar and half of the sharp cheddar cheese over the noodles. Add the remaining macaroni mixture on top, then cover with the rest of the aged cheddar and sharp cheddar. Sprinkle the whole wheat breadcrumbs evenly over the entire surface.
• Place the assembled casserole in the oven at 350°F (175°C) and bake for 25–30 minutes, or until the macaroni and cheese is bubbling and the breadcrumbs are golden brown. Remove from the oven and allow it to rest for 5 minutes before serving. For an extra touch, I sometimes broil the top for 1-2 minutes at the end for a super crispy crust.