Butternut Squash Mac and Cheese

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This deliciously cheesy Butternut Squash Mac and Cheese is packed with cozy fall squash and melty cheese, making it a comforting vegetarian meal or side dish to warm up to on cold nights.

If you love mac & cheese, try my pumpkin mac and cheese next! You may also like my Sloppy Joe Casserole.

A white dish with mac and cheese made with added roasted butternut squash.

If you love Trader Joe’s Butternut squash mac and cheese then you will love this recipe. You no longer have to wait all year for it! Yay! So go ahead, make this fall-inspired Butternut Squash Macaroni and Cheese recipe, and you are guaranteed to please everyone around the dinner table. The combination of slightly sweet, nutty butternut squash with the gooey melted cheese and tender pasta is my favorite way to enjoy macaroni and cheese!

Looking for more delicious squash recipes? Try this Butternut Squash Mushroom Risotto or this Butternut Squash Salad recipe.

Recipe Summary

Family-friendly: My kids love mac and cheese, and with this recipe, I can sneak in an extra serving of vegetables. But the truth is, this butternut squash macaroni is SO tasty they don’t even care that it’s made with veggies.
Perfect for fall: Butternut squash always gets me in the fall spirit. Cozying up to a bowl of roasted butternut squash soup or enjoying this unique hasselback butternut squash.

Ingredients you’ll need

ingredients to make mac and cheese with butternut squash.

This butternut squash macaroni and cheese recipe is made by combining some simple kitchen staples and one of my favorite seasonal ingredients, squash! Full measurements are listed further down in the recipe card.

Butternut squash: Roasting cubes of the butternut squash caramelize it and bring out its natural sweetness.
Cooking spray: For roasting the butternut squash.
Kosher salt & pepper: To enhance the flavor of the squash as it cooks.
Elbow macaroni: This noodle shape is perfect for holding all of the cheesy sauce, so every bite is filled with incredible taste.
Olive oil: For sautéing the garlic and starting the sauce.
Garlic: Provides extra savory flavor.
Flour: Helps to thicken the cheese sauce.
Milk: Adds moisture and helps thin the sauce so it spreads evenly over the noodles.
Cheese: We’re using two types of shredded cheese (sharp cheddar cheese and parmesan cheese) for an amazing depth of flavor.

Substitutions

Replace the squash: Try using fresh pumpkin or sweet potato instead of the squash for a slightly different flavor.
Pasta: Use protein pasta for an extra boost of protein. You can also use gluten-free pasta to make this entire dish gluten-free friendly.
Flour: I typically use a gluten-free all-purpose flour, but regular all-purpose flour also works great.
Milk: Any milk will work, but whole milk will make for a richer sauce.
Cheese: Instead of just sharp cheddar cheese, use half sharp cheddar and half Gruyere cheese to change things up.

How to make it

Follow the step-by-step process below on how to make this recipe. For the full ingredients quantities and printable recipe instructions, scroll to the recipe card at the bottom of this post.

Roasted cubed butternut squash on a sheet pan.

Step 1: Preheat the oven to 400ºF and line a large sheet pan with parchment paper. Spread the cubed butternut squash onto the pan and spray with cooking oil spray. Sprinkle it with salt and pepper. Bake for 25-30 minutes, or until tender.

Pouring milk into a blender with roasted butternut squash.

Step 2: Meanwhile, boil the pasta in salted water according to package directions to al dente. Drain and set aside. To make the sauce, heat the oil in a small saucepan over medium heat. Sauté the garlic for 30 seconds, then stir in the flour. Add the milk little by little and continuously whisk until no visible lumps. Allow the sauce to bubble for around 5 minutes to thicken. Stir in the cheese and whisk until incorporated. At this point, the sauce should be thickened to coat the back of your spoon. Don’t worry if it’s not smooth, it will be perfect after blending. Transfer the sauce to a blender and add half of the roasted butternut squash. Blend until smooth.

Pouring sauce over macaroni noodles in a white baking dish.

Step 3: To assemble the dish, add the pasta to a large baking dish. Pour the sauce over and add the remaining half of the roasted butternut squash. Stir to combine.

Butternut squash Mac and cheese in a white casserole dish.

Step 4: Sprinkle with parmesan cheese and bake for 25 minutes, or until bubbly.

Rena’s Tips

Recipe tips

Time-saving tip: You can usually find pre-cubed squash seasonally in the produce department at your grocery store, which eliminates most of the work in this recipe! You can also use frozen cubed butternut squash, just thaw before using.
Peeling butternut squash: To make it easier to peel your squash, microwave it for 1-2 minutes. Poke a few holes in it with a fork beforehand to allow for the release of steam.
Boil pasta to al dente: The macaroni noodles will continue to cook in the oven, so it’s important to only boil until al dente (slightly undercooked) to keep them from becoming mushy.
Freshly grated cheese: If you have the time, I recommend shredding and grating your cheese from a block so that the cheese gets nice and melty. The bagged pre-shredded cheeses are coated in anti-caking agents and just don’t melt as smoothly. They also aren’t as flavorful!
Keep it warm: If you’re serving this as part of a holiday spread, keep it warm by transferring it to a crockpot set on warm. Spray the crockpot insert with nonstick cooking spray to prevent the noodles from sticking to the bottom.

a white dish with mac and cheese made with cheese and added butternut squash.

Common questions

How do you keep mac and cheese creamy when reheating?

To keep the mac and cheese from drying out when reheating either in the microwave or on the stovetop, stir 1 tablespoon of milk into each 1 cup of mac and cheese before reheating.

Do I cover the dish before baking?

No, you will not want to cover the pasta dish while baking because we want the top to get golden brown and slightly crispy.

What to serve with butternut squash pasta?

Serve this as a vegetarian main course with a fresh green salad, air fryer broccoli or garlic roasted veggies, and some crusty bread. It’s also great as a side dish paired with roasted turkey breast, homemade meatloaf, or garlic butter chicken.

Storage recommendations

Storing: Store leftovers in an airtight container in the refrigerator for 3-4 days.
Reheating: Before reheating, stir in a bit of milk to make the pasta creamier. Reheat in the microwave in small increments, covered until heated through. Or on low heat on the stovetop until warmed through.