Butternut Squash Mac and Cheese

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Published Nov 09, 2026

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This creamy butternut squash mac and cheese gives classic comfort food a fall upgrade, and it’s delicious! Loaded with tender noodles baked in a silky sauce with four kinds of cheese, homemade butternut squash purée, and a crispy, toasted breadcrumb topping.

Butternut squash mac and cheese served in a bowl with a fork on the side.

Creamy, Cheesy Butternut Squash Mac and Cheese

I’ve been on a comfort food kick lately with Buffalo mac and cheese, baked mostaccioli, and turkey tetrazzini, all in rotation. So, this four-cheese butternut squash mac and cheese recipe fits right in! It’s a seasonal twist on baked mac and cheese, with butternut squash puree stirred into a rich sauce made with shredded cheddar, mozzarella, Parmesan, and cream cheese. I toss the sauce with macaroni, top with panko, and bake until golden and crisp.

I already love roasted squash in my butternut squash lasagna, so I roast and blend the butternut squash myself for this recipe, too, for a smooth sauce and extra flavor. But canned squash purée works too!

This would be a great make-ahead holiday side, and I can already picture it next to this year’s Thanksgiving turkey. It’s definitely crowd-friendly, and this butternut squash mac and cheese tastes even better reheated.

Butternut squash mac and cheese in a baking dish.

Ingredients Needed

Gather your ingredients to make this creamy butternut squash macaroni and cheese. See the recipe card for the exact measurements.

Butternut squash mac and cheese ingredients with text labels.

Pasta – I like cavatappi (pictured here), but you can use another short pasta shape or keep it classic with elbow macaroni.
Butter, Flour, and Milk – These ingredients combine to make béchamel sauce, the thickening base for the creamy cheese sauce. You’ll whisk the flour and butter to make a roux before adding the milk.
Butternut Squash Purée – You can use canned purée or make it from scratch; see the recipe card for instructions. I would make the purée before assembling the mac and cheese.
Cream Cheese – Use the kind that comes in bricks. Full-fat cream cheese makes a richer, silkier sauce. For easy mixing, take the cream cheese out of the fridge and let it soften at room temperature.
Shredded Cheese – I use a combination of shredded sharp cheddar and melty mozzarella for flavor and a perfect cheese pull. Other good melting cheese choices for mac and cheese include shredded Havarti, Provolone, Gruyère, and Gouda.
Parmesan – Freshly grated Parmesan is best. You can skip it if need be, or substitute Pecorino or additional shredded cheese.
Dijon Mustard – Adds a little sharp contrast to the cheese sauce. Yellow mustard works too, or you can add about ¼ teaspoon of mustard powder instead of prepared mustard.
Spices – Garlic powder, paprika, and ground nutmeg (if you have fresh nutmeg to grind, even better!).
Breadcrumbs – I use Panko for the big, crunchy crumbs. Regular breadcrumbs also work. I’ll sometimes swap panko crumbs with crushed saltines, croutons, or Ritz crackers, like the topping on my Ritz chicken casserole. You’ll combine the crumbs with melted butter and extra grated Parmesan to make the crispy topping.

How to Make Butternut Squash Mac and Cheese

If you’re making the butternut squash purée from scratch, prepare it before you start on the mac and cheese. See the Homemade Butternut Squash Purée section below, then follow these steps:

Drained cavatappi pasta in a colander. — Cook and drain the pasta.

Pouring milk into a saucepan while whisking flour and butter to make roux. — Cook and drain the pasta.

Cook the noodles. Bring a pot of salted water to a boil. Cook your noodles for about 2 minutes less than the package’s recommended cooking time. You want the pasta slightly undercooked, since it finishes cooking in the oven afterward. Drain, and I like to toss the cooked noodles with a little olive oil to keep them from sticking together before setting them aside.
Make the béchamel. In a saucepan, start by whisking flour with melted butter to make a roux. Cook it for a minute, then slowly whisk in the milk. Simmer for 3-5 minutes, whisking often, until thickened.
Finish the butternut squash cheese sauce. Lower the heat and stir in the butternut squash purée, cream cheese, Dijon mustard, and spices. Then, off the heat, fold in the shredded cheddar, mozzarella, and Parmesan cheese. Season the sauce with salt and a scrunch of freshly cracked pepper to taste.
Combine. Stir the cooked pasta into the cheese sauce to coat. Then, transfer the mac and cheese mixture to a greased casserole dish.
Add the topping and bake. Finally, mix the breadcrumb topping ingredients and sprinkle them evenly over the mac and cheese. Bake the butternut squash mac and cheese uncovered at 375ºF for 20-25 minutes, until the cheese is bubbly and the topping is a crispy golden brown. Rest the casserole for a few minutes before serving.

Homemade Butternut Squash Purée

Roasting concentrates the squash and yields a thicker, more flavorful purée than boiling. You can even roast and purée the squash 3-4 days in advance and keep it in the fridge until you’re ready to use it.

Get ready to roast. Cut your butternut squash in half lengthwise, then scoop out the stringy pulp and seeds (see how to cut butternut squash in my roasted butternut squash recipe). Place the squash halves cut-side down on a parchment-lined baking sheet.
Roast. Roast the squash at 425ºF for 40-50 minutes. Test for doneness using a fork; the squash should be easy to pierce and tender throughout.
Blend. Wait a few minutes for the squash to cool, then scoop out the flesh and transfer it to a food processor. You can also use a blender with an open lid. Blend the squash until it’s completely smooth. If it seems a bit watery, drain the purée through a sieve before you use it. Don’t add water or milk while blending, as it dilutes the flavors.
Measure out the purée. Measure one cup of purée for the mac and cheese. If you have a lot of it left over, you can use it for other recipes, like my butternut squash soup!

This butternut squash cheese sauce is also a great way to use up leftover baked butternut squash. In this case, you can skip the roasting step and add it straight to the blender. Make sure you have at least one cup of purée for the sauce.

Scooping butternut squash mac and cheese from a baking dish.

Recipe Tips and Variations

Do not overcook the pasta. Stop cooking the pasta before it reaches al dente so it can finish cooking in the mac and cheese without getting mushy or overcooked.
The cheese sauce should be loose before baking. The pasta absorbs the sauce while the mac and cheese bakes, so it’s best if it’s a little loose beforehand.
For an extra-crispy topping, broil the butternut squash mac and cheese for 1-2 minutes right at the end of baking. Just keep a close eye on it; the breadcrumbs can go from crisp to burnt quickly!
Let the finished mac and cheese rest and set on the counter for 5 minutes before serving. This avoids a very hot bite and keeps the casserole creamy.
To save time, you can roast pre-cut squash, frozen squash cubes, or use canned squash purée.
You can make this gluten-free by using your favorite gluten-free pasta and substituting the all-purpose flour with gluten-free flour in the roux.
Get creative with add-ins. Try a smoky variation with chopped cooked bacon, pulled pork, or smoky chipotle powder stirred in.
Add sage. If you’d like, blend fresh sage into the purée or add it to the finished mac and cheese mixture. It goes nicely with the squash and adds another layer of flavor.
Swap the butternut squash. You can make this recipe with any type of squash, including delicata, acorn, etc. Roasting times may vary slightly depending on the size. You can also use canned pumpkin or my slow cooker pumpkin purée to make pumpkin mac and cheese.

Slow Cooker and Instant Pot Options

While I’m not one to pass on a crispy-topped pasta bake, if the oven is occupied, I love adapting this butternut squash mac and cheese recipe to my slow cooker or pressure cooker:

Slow cooker: So easy, and you don’t even need to cook the pasta first. Instead, rinse the noodles with cold water. Whisk melted butter with flour and milk to make the roux, then add all the ingredients to the crock pot. Stir, and cook on Low for 1 hour, adding an extra half-hour as needed until the pasta is tender.
Instant Pot: Add salted water and pasta to the pot, then cook on High Pressure for 4 minutes, and do a quick release. Switch the pot to Sauté, and stir in cream cheese and puréed squash. Once melted, add the remaining cheeses and ingredients, and simmer until fully melted and smooth.

And if you’re pining for that crispy topping, go ahead and toast the buttery breadcrumbs in a dry skillet, then sprinkle them on top when serving.

A fork lifting a serving of butternut squash mac and cheese from a bowl.

Serving Butternut Squash Mac and Cheese

The cozy flavor of roasted butternut squash makes this mac and cheese the perfect fall weeknight dinner. As a main or a side, these are some easy serving ideas:

Bread on the side: Serve with garlic bread, copycat Texas Roadhouse rolls, or butter swim biscuits.
Holidays: Enjoy this fall-themed mac and cheese as a side to a spatchcock turkey or a prime rib roast, complete with cranberry sauce, stuffing, and green bean casserole.
Kid-friendly: Pair it with crispy chicken tenders or chicken schnitzel.

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Storing and Reheating Leftovers

Refrigerate. Cover and refrigerate the leftover butternut squash mac and cheese for up to 4 days. The topping will lose its crunch over time, but the flavors will still be great.
Reheat. Warm servings in the microwave, or you can reheat larger portions in a 350ºF oven (best for crisping up the top again).