This Butternut Squash Mac and Cheese takes everything you love about classic mac and cheese and gives it a cozy fall twist. Creamy, cheesy, and topped with crisp breadcrumbs, it works beautifully as a vegetarian main or a comforting side.
Mac and cheese is one of the ultimate comfort foods — warm pasta smothered in a velvety cheese sauce is hard to beat. This version adds roasted butternut squash for a sweet, nutty note and a beautiful orange hue. The squash brightens the flavor and makes the dish feel especially appropriate for autumn and winter gatherings.
If you love squash, this baked mac and cheese is an excellent way to showcase it. The recipe is more involved than a simple stovetop mac, but the layered flavors and the crunchy breadcrumb topping make the effort worthwhile.
Why you’ll love this recipe:
- Creamy, cheesy sauce balanced by the natural sweetness of roasted butternut squash and a crunchy breadcrumb topping.
- A warm, comforting dish that works as a vegetarian main or a hearty side.
- Make-ahead friendly: you can roast the squash and prepare the purée in advance to streamline assembly.
Recipe ingredients
This baked mac and cheese combines a smooth cheese sauce, roasted butternut squash purée, cooked pasta, and a buttery breadcrumb topping.
- Butternut squash purée: Roasting the squash yields the best flavor and texture. If short on time, canned purée can be used, though homemade tastes fresher.
- Pasta: 8 ounces (1/2 lb) of short pasta such as shells, elbow macaroni, cavatappi, or rotini.
- Milk: Whole milk gives the richest, creamiest sauce.
- Butter: Used for sautéing aromatics, making the roux, and tossing with breadcrumbs for browning.
- Cheese: Freshly grated cheese melts best—sharp white cheddar is recommended; fontina, gruyère, or parmesan also work well.
- Flour: Two tablespoons to make the roux and thicken the sauce.
- Shallot and garlic: Optional, but they add depth and savory balance to the sweet squash.
- Smoked paprika and thyme: Smoked paprika brings a subtle smokiness and thyme provides a fresh herbal lift.
See the recipe card below for the full ingredient list and exact quantities.
How to make butternut squash macaroni and cheese
The dish is built in a few straightforward parts: roast and purée the squash, cook the pasta, make a creamy cheese sauce (a béchamel-based sauce thickened with flour), combine everything, top with cheese and breadcrumbs, then bake until golden and bubbly. You can assemble the casserole a few hours ahead of time and bake when needed.
Pro tip: Make the roasted butternut squash purée up to a few days ahead and refrigerate it. Homemade purée delivers the best flavor and a smooth, velvety texture.
Full instructions are in the recipe card below.
- Roast the butternut squash until very tender, then scoop the flesh into a blender or food processor with 1/2 cup of the milk and blend until smooth. The purée should be silky.
- Cook the pasta 2 minutes less than the package directions so it stays slightly underdone before baking. Drain well.
- In a large saucepan over medium heat, melt 1 tablespoon of butter and sauté the finely chopped shallot for 2–3 minutes until softened. Add minced garlic and smoked paprika and cook for 30 seconds more.
- Add 2 tablespoons more butter to the pan and melt. Sprinkle in 2 tablespoons of flour and whisk constantly until the roux is golden and fragrant, about 1 minute.
- Off the heat, add about one-third of the milk in a slow stream while whisking to make a smooth paste. Whisk in the remaining milk, then return the pan to medium heat. Bring to a boil while whisking, then reduce the heat and simmer until thickened, about 3–5 minutes.
- Remove from heat and stir in 1 1/2 cups of grated cheese, the butternut squash purée, and chopped thyme. Season with salt and pepper to taste.
- Toss the cooked pasta with the cheese-squash sauce until evenly coated. Transfer to a greased 8×8″ baking dish and sprinkle the remaining 1/2 cup of cheese over the top.
- Melt the last tablespoon of butter, mix with 1/2 cup panko breadcrumbs, and sprinkle evenly over the casserole. Bake at 350°F until bubbly and golden, about 20–30 minutes. If the top browns too quickly, tent with foil.
Recipe FAQs
It’s rich and creamy with a sweet, slightly nutty undertone from the squash. Aromatics like shallot and garlic add savory depth, smoked paprika contributes a hint of smoke, and thyme brings a fresh herbal note.
Roasting develops the best flavor and texture, but you can also cube and boil the squash until tender. Canned purée will work in a pinch but lacks the brightness and velvety texture of freshly roasted purée.
Sharp white cheddar is a great choice for flavor and meltability. Fontina, gruyère, and parmesan are all good options, and combining cheeses adds complexity. Avoid pre-grated cheese for best melting results.
Short pasta with curves or ridges holds the sauce well. Elbows, shells, cavatappi, and rotini are ideal.
Serving suggestions
This dish stands on its own but pairs well with simple salads, roasted vegetables, or roasted meats. For a lighter meal, serve with a crisp green salad. To add nutrition, swap in whole wheat pasta or stir in cooked spinach or kale before baking.
- Serve as a vegetarian main with a side salad and roasted asparagus or Brussels sprouts.
- Serve as a side alongside roasted chicken, turkey breast, or seared steak.
- Substitute pumpkin purée for a seasonal variation.
Recipe notes
- Make ahead: Roast and purée the squash up to a few days in advance and refrigerate.
- You can skip baking and serve the pasta tossed with the warm sauce for a quick stovetop version.
- Make it more nutritious by using whole wheat pasta and/or adding cooked spinach or kale.
- Store leftovers in the refrigerator for up to 3 days.
More butternut squash recipes you’ll love
- Butternut squash quinoa salad
- Cinnamon roasted butternut squash
- Creamy butternut squash soup
- Roasted butternut squash and pear soup
Did you try this recipe? If so, leave a review below and tag @flavorthemoments on social media so I can see what you made.
Butternut Squash Mac and Cheese
Creamy, cheesy baked mac and cheese with roasted butternut squash folded into the sauce and a crispy breadcrumb topping — a perfect fall comfort dish.
Ingredients
- 1 tablespoon extra virgin olive oil
- 1.5 lbs butternut squash (yields about 1 1/2 cups purée)
- 2 1/2 cups whole milk, divided
- 8 ounces short cut pasta (shells, elbows, etc.)
- 4 tablespoons unsalted butter, divided
- 1 small shallot, finely chopped
- 2 cloves garlic, minced
- 1/2 teaspoon smoked paprika
- 2 tablespoons all-purpose flour
- 2 cups grated white cheddar cheese, divided
- 1 tablespoon chopped fresh thyme (or 1.5 teaspoons dried)
- Salt and pepper to taste
- 1/2 cup panko breadcrumbs
Instructions
Roast the butternut squash
- Preheat the oven to 400°F. Line a rimmed baking sheet with foil. Trim the squash, cut in half lengthwise, remove seeds, brush with olive oil, and place cut-side down on the baking sheet. Roast 30–40 minutes or until very tender.
- Let cool slightly, then scoop the flesh into a blender or food processor with 1/2 cup of the milk and process until smooth. (Purée can be refrigerated for a few days.)
Prepare the mac and cheese
- Grease an 8×8″ baking dish and preheat the oven to 350°F.
- Cook the pasta until very al dente (about 2 minutes less than package directions). Drain well.
- In a medium saucepan, melt 1 tablespoon butter over medium heat. Sauté the shallot 2–3 minutes until softened, then add garlic and smoked paprika and cook 30 seconds more.
- Add 2 tablespoons butter, then sprinkle in the flour and whisk constantly until golden and bubbly, about 1 minute. Remove from heat and slowly whisk in about one-third of the milk to form a smooth paste. Whisk in the remaining milk, return to medium heat, bring to a boil while whisking, then simmer until thickened, 3–5 minutes.
- Remove from heat and stir in the squash purée, 1 1/2 cups of the cheese, and thyme. Season with salt and pepper. Add the pasta and stir to coat.
- Transfer to the prepared baking dish, sprinkle the remaining 1/2 cup cheese on top. Melt the final tablespoon of butter, toss with the breadcrumbs, and sprinkle over the casserole. Bake 20–30 minutes until bubbly and golden. If the top browns too quickly, tent with foil.
Notes
- Make the squash purée ahead to save time.
- Try different cheeses like fontina, gruyère, or parmesan for varied flavor.
- You can skip baking and serve the pasta immediately after tossing with the sauce.
- Add cooked spinach or kale or use whole wheat pasta for a more nutritious version.
- Store leftovers in the refrigerator for up to 3 days.
Nutrition (estimate)
Calories: 528 kcal; Carbohydrates: 54 g; Protein: 19 g; Fat: 27 g; Saturated Fat: 14 g. Nutrition values are estimates and intended as a guideline only.