Baked Butternut Squash Mac and Cheese: Creamy, Cheesy, and Cozy Comfort Food

When you’re craving something warm, cheesy, and comforting, there’s nothing quite like a baked mac and cheese fresh out of the oven. This butternut squash mac and cheese version gets a little upgrade with creamy butternut squash purée blended right into the sauce for extra richness and that subtle hint of sweetness that makes it so good.

Serving of baked butternut squash mac and cheese on rustic plate with thyme.

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Mac and cheese has always been one of those dishes that feels like home. I’ve made it every which way, stovetop, baked, extra crispy, extra creamy. But this butternut squash mac and cheese might be the one that wins them all over. I love that it still has everything you expect from a classic mac and cheese, all the gooey cheese, a buttery topping, the comfort, just with a little something extra that makes it feel special.

It’s a vegetarian dinner that feels just as hearty as the classic, with plenty of sharp cheddar cheese and a golden breadcrumb topping that turns crisp and irresistible as it bakes. It fits perfectly into a weeknight dinner, a holiday menu, or any cozy night when you just want comfort food that tastes like home.

Why You Will Love This Recipe

  • Creamy and cheesy: A rich, silky sauce made with butternut squash purée and sharp cheddar cheese gives this butternut squash mac and cheese that perfect balance of comfort and flavor.
  • Family favorite: It’s one of those meals everyone reaches for seconds of, the kind of comfort food that disappears fast once it hits the table.
  • Easy to make: Simple ingredients and pantry staples make this a weeknight dinner that still feels special.
  • Versatile: Serve it as a main for a vegetarian dinner, or add it to your holiday menu as a cozy side dish for your next Thanksgiving feast.
  • Golden and cozy: The baked breadcrumb topping turns crisp and buttery while the inside stays creamy and loaded with gooey cheese.
Spoon lifting creamy baked butternut squash mac and cheese from rectangular casserole dish.

Ingredients

Flat lay of ingredients for butternut squash mac and cheese on marble with sage napkin.
  • Butternut squash: Fresh or frozen butternut squash both work. Steaming keeps the flavor mild, while roasted squash adds a deeper, nutty note.
  • Cheese: Use sharp cheddar cheese for that bold, classic flavor, plus a little mozzarella and Parmesan for a creamy, melty finish.
  • Spices: A touch of nutmeg and paprika balances the sweetness of the squash and gives the sauce a warm, cozy color.
  • Breadcrumb topping: Buttered breadcrumbs bake up golden and crisp, the best contrast to that creamy inside.

See the recipe card for the complete list of ingredients and quantities.

Instructions

Steamed butternut squash cubes in metal colander over marble surface with green napkin.

Step 1: Add diced squash to a steamer basket set over simmering water. Cover and steam for 10-12 minutes, or until fork-tender.

Smooth butternut squash purée in clear blender jar with visible texture.

Step 2: In a blender or food processor, combine the steamed squash, milk, melted butter, salt, pepper, nutmeg, and paprika. Blend until smooth and creamy.

Creamy butternut squash mac and cheese mixture in cream pot being stirred with wooden spoon.

Step 3: Pour the blended sauce into a large pot. Set over medium-low heat and whisk in cheddar, mozzarella, and Parmesan until melted and smooth. Add the drained pasta to the sauce and stir until evenly coated.

Rectangular baking dish filled with mac and cheese topped with breadcrumbs before baking.

Step 4: Transfer the mac and cheese to a 9×13-inch baking dish. In a small bowl, combine breadcrumbs, melted butter, salt, pepper, and thyme. Sprinkle evenly over the top.

Top-down view of baked butternut squash mac and cheese with golden breadcrumb crust.

Step 5: Bake at 375℉ for 20-25 minutes, until bubbling around the edges and the topping is crisp and golden. Let rest for 5 minutes before serving.

Expert Tips

  • Grate your own cheese. Pre-shredded cheese doesn’t melt as smoothly. Freshly grated sharp cheddar gives the sauce a cleaner, creamier texture.
  • Cook the macaroni just short of al dente so it holds its bite after baking.
  • Bake uncovered for a crisp, golden top, or cover loosely with foil for a softer crust.
  • Assemble earlier in the day, refrigerate, and bake right before serving. Add 10 extra minutes of bake time if it’s cold from the fridge.

Serving Ideas And Variations

Serve this butternut squash mac and cheese with something fresh and light on the side, a green salad with lemon dressing, roasted broccoli, or garlic bread. It’s rich and satisfying on its own, so a simple side keeps the balance just right. This chopped chicken salad is our family’s favorite.

For a variation, stir in sautéed spinach, caramelized onions, or roasted mushrooms before baking. Each adds depth and texture without changing what makes this creamy pasta so comforting. If you like the butternut squash mac and cheese, these mac and cheese bites are a fun party version to keep on hand for game days and gatherings.

Close-up of butternut squash mac and cheese in stoneware bowl with crispy topping.

More Vegetarian Dinner Ideas

  1. Homemade beet ravioli that looks like it came from a restaurant, but made right in your kitchen. Elegant, colorful, and filled with creamy goat cheese, the perfect dish when you want something a little special.
  2. Crispy on the outside, soft on the inside, these halloumi burgers are an easy vegetarian favorite. Pan-fried golden and stacked high, they’re quick enough for a weeknight and satisfying enough for everyone at the table.
  3. This loaded green bean casserole bakes into a creamy, tender dish with a golden garlic butter crumb that adds the perfect crunch. It’s made without mushroom soup or any canned ingredients, giving you a fresh, festive side that always feels special on the holiday table.
  4. This pumpkin sage mac and cheese bake is an easy family dinner with warm flavors and a rich, baked finish. It holds up beautifully for meal prep, so you can enjoy it right away or reheat it during the week with the same steady, satisfying flavor.
  5. This one-pot broccoli cheddar soup is creamy, smooth, and deeply comforting, the kind of dinner that feels steady and familiar after a long day. It comes together into quickly and works just as well for quiet weeknights as it does for leftovers the next day.

Tried this butternut squash mac and cheese? Please rate the recipe and leave a comment below to let us know how they turned out. Your feedback helps others find and enjoy it too!

Baked Butternut Squash Mac and Cheese

Plated portion of butternut squash mac and cheese showing creamy sauce and toasted crumbs.
This baked butternut squash mac and cheese is everything you love about the classic, creamy sauce, gooey cheese, and a golden breadcrumb crust, with a cozy touch. The butternut squash purée adds warmth and depth, making it a perfect vegetarian dinner for weeknights, holidays, or anytime you’re craving real homemade comfort food.
Prep Time 20 minutes
Cook Time 45 minutes
Total Time 1 hour 5 minutes
Serving Size 6

Equipment

  • Large pot
  • Steamer basket or colander
  • Blender or food processor
  • Baking dish 9×13-inch
  • Wooden spoon

Ingredients

For the Pasta and Sauce

  • 12 ounces elbow macaroni about 4 cups uncooked
  • 2 ½ cups butternut squash peeled and cut into 1-inch cubes
  • 2 tablespoons unsalted butter
  • 1 ½ cups milk whole milk preferred
  • Salt and pepper to taste
  • ½ teaspoon ground nutmeg
  • ½ teaspoon smoked paprika optional, for color
  • 2 cups sharp cheddar cheese shredded
  • ½ cup mozzarella shredded
  • ½ cup Parmesan cheese grated

For the Topping

  • ½ cup breadcrumbs plain or panko
  • Salt and pepper to taste
  • 1 tablespoon butter melted
  • 1 teaspoon fresh thyme finely chopped

Instructions

  • Add diced squash to a steamer basket set over simmering water. Cover and steam for 10-12 minutes, or until fork-tender.
  • Meanwhile, bring a large pot of salted water to a boil. Cook the macaroni 1 minute less than the package directions for an al dente texture. Drain and set aside.
  • In a blender or food processor, combine the steamed squash, milk, melted butter, salt, pepper, nutmeg, and paprika. Blend until smooth and creamy.
  • Pour the blended sauce into a large pot (you can reuse the pasta pot after draining). Set over medium-low heat and whisk in cheddar, mozzarella, and Parmesan until melted and smooth.
  • Add the drained pasta to the sauce and stir until evenly coated. The mixture should be rich, creamy, and thick.
  • Transfer the mac and cheese to a 9×13-inch baking dish. In a small bowl, combine breadcrumbs, melted butter, salt, pepper, and thyme. Sprinkle evenly over the top.
  • Bake at 375℉ for 20-25 minutes, until bubbling around the edges and the topping is crisp and golden. Let rest for 5 minutes before serving.

Notes

  • Use frozen butternut squash cubes to save prep time. Just steam directly from frozen.
  • Stir in ¼ cup cream cheese with the cheddar for a richer sauce.
  • For a shortcut, skip baking and serve straight from the stovetop as creamy mac and cheese.
  • Leftovers keep 3-4 days in the fridge and reheat best in the oven at 350°F (covered) for 10-15 minutes.

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