Creamy, cheesy, and comforting, this Butternut Squash Mac and Cheese is one of my favorite fall dishes. Tender pasta shells are tossed in a creamy sauce made with roasted butternut squash, roasted garlic, sharp cheddar, and smoky Gouda. It’s then finished with a crisp, buttery panko topping for that perfect texture contrast.
The butternut squash does double-duty here: it adds a subtle sweetness and naturally thickens the cheese sauce. It’s also a great make ahead dish, perfect for the holidays!
Quick Look at the Recipe
- Prep Time: 20 minutes, Cook Time: 1 hour 10 minutes
- Total Time: 1 hour 30 minutes
- Method: Oven-roasted, stovetop sauce, baked
- Main Ingredients: Butternut squash, pasta shells, cheddar, Gouda
- Flavor Profile: Savory, cheesy, subtly sweet, warm flavors
- Ideal for: Thanksgiving sides, fall comfort food, potlucks, make ahead
Ingredient Notes
- Butternut squash: One small squash, about 1 to 1½ pounds. Once roasted, you’ll scoop out about 1½ cups of soft flesh, which is just the right amount for a creamy sauce that still tastes cheesy.
- Roasted garlic: A whole head, roasted right alongside the squash. It blends straight into the puree for a sweet, mellow garlic flavor throughout the mac and cheese with butternut squash.
- Pasta shells: I like medium pasta shells because they scoop up all that sauce.
- Cheeses: Yellow cheddar for that classic sharp flavor, and Gouda for a smooth melt and a hint of smokiness. Grab blocks and shred them yourself for a cheesier butternut squash mac and cheese.
- Dairy: Mostly heavy cream, plus some whole milk. Cream holds up better to the thick squash puree than milk alone and keeps the sauce rich and silky.
- Seasonings: Fresh thyme, rosemary, garlic powder.
- Ground nutmeg might sound unusual in mac and cheese, but it pairs beautifully with butternut squash.
- Panko breadcrumbs tossed in browned butter with a little minced rosemary.
- Unsalted butter, all-purpose flour, olive oil, salt, and pepper.
As always, ingredient quantities can be found in the recipe card down below.
Substitutions and Variations
- Canned squash puree: Use about 1½ cups of canned butternut squash puree, a little less than one 15-ounce can.
- Pasta: Any short pasta works, like elbows, cavatappi, or rigatoni.
- Cheese swaps: Try Gruyere, fontina, or white cheddar in place of the Gouda.
- Add-ins: Crispy bacon, pancetta, or sautéed spinach are all great.
- For an extra cozy twist, brown the butter with a fresh sage leaf before tossing it with the panko.
How to Make Butternut Squash Mac and Cheese
Step 1 | Roast the squash and garlic
Slice the top off the garlic head to expose the cloves. Drizzle with olive oil, season with salt and pepper, and wrap tightly in foil. Halve the butternut squash from top to bottom, and scoop out the seeds. Place cut side up on a baking sheet, drizzle with olive oil and season well. Roast both the squash and garlic at 400°F for about 50 minutes, until very tender.
Scoop the squash from the skin and squeeze the garlic cloves from their skins. Blend both with milk to make a smooth and thick puree.
Tip: Roasting the squash cut side up allows excess moisture to evaporate, concentrating the flavor and creating a thicker puree.
Step 2 | Make the butternut squash cheese sauce
While the squash roasts, cook the pasta until just shy of al dente (it will finish cooking in the oven). Save some starchy pasta water before draining.
In a large oven-safe pan, melt the butter over medium heat. Whisk in the flour (only 1 tablespoon) and cook for 2-3 minutes to get rid of the raw flour taste. Then add garlic powder, nutmeg, thyme, and rosemary for another 1-2 minutes to bloom the seasonings.
Stir in the butternut squash puree, then gradually pour in the heavy cream and milk. Bring it to a gentle simmer. It will start to thicken.
Turn the heat to low and stir in the freshly shredded cheddar and Gouda cheeses until melted and smooth, just a few seconds. Turn off the heat. Season to taste. Tip: High heat can make the cheese sauce turn grainy and oily.
Step 3 | Assemble the mac and cheese
Fold in the cooked shells into the butternut cheese sauce. Add a few splashes of the reserved pasta water to loosen it up until creamy and smooth. If needed, transfer to a 9×13 baking dish.
Make the breadcrumb topping: Brown the butter in a small pan, toss it with the panko and herbs.
Step 4 | Bake at 375°F
Top the mac and cheese with more shredded cheese and sprinkle the prepared breadcrumbs evenly. Bake your butternut squash mac and cheese uncovered at 375°F for 20-25 minutes, until bubbling and golden.
Tips for Success
- Just a pinch of nutmeg! A little goes a long way. It adds really nice, warm flavors. You can always add more later.
- Use freshly shredded cheese. Pre-bagged shredded cheese is coated with added starches to keep it from clumping in the packaging, which can actually make the sauce gritty. Freshly shredded cheese melts smoother and creamier.
- Go easy on the flour. This recipe uses less flour than a typical roux because the squash puree acts as its own thickener.
- Adjust with pasta water. The puree is thick, so loosen the sauce with starchy pasta water until it’s creamy and smooth. You can also add more milk.
- Seasoning. Squash and pasta both soak up salt, and the cheese is already salty. so taste before seasoning further. It should taste slightly salty on its own.
Make Ahead, Storing, Reheating
Make ahead: Roast and blend the butternut squash up to 3 days ahead and refrigerate. You can also assemble the whole dish (without the breadcrumbs) up to a day ahead.
Storing: Leftover butternut squash mac and cheese keeps in an airtight container in the fridge for 3 to 4 days. It actually stores really well, and the flavors get even better overnight!
Freezing: Freeze the baked and cooled mac and cheese in portions for up to 3 months. Thaw overnight in the fridge before reheating.
Reheating: Stir in a splash of milk to loosen the sauce, then cover with foil and warm at 350°F for 20+ minutes. For single portions, the microwave works great with a splash of milk, stirring halfway.
Recipe FAQs
Yes. Roast the frozen cubes at 400°F until tender and lightly caramelized, then blend as directed. Steamed or boiled squash works in a pinch, but it holds more water, so the sauce may need less milk.
Absolutely. Cook the pasta fully to al dente, stir it into the sauce, and serve it right away. You’ll skip the crispy topping, but it’s just as creamy.
The squash adds a mild, nutty sweetness and color without overpowering the dish. You still get plenty of cheddar and Gouda flavor, making it an easy way to sneak in some veggies.
Usually the heat was too high when the cheese went in, or pre-shredded cheese was used. Add the cheese over low heat and stir just until melted.
Pairing and Serving Ideas
- Mains: Serve it alongside roast turkey, my Dutch Oven Roast Chicken, Apple Cider Pulled Pork, or Dutch Oven Pot Roast.
- Veggie sides: For Thanksgiving, par this butternut mac and cheese with my Fresh Green Bean Casserole, or serve with these easy Sauteed Brussels Sprouts.
- Salad: Something crisp and bright like my Fall Harvest Salad or Kale Apple Slaw balances all that creaminess.
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Creamy Butternut Squash Mac and Cheese
Ingredients
For the butternut squash puree:
- 1 to 1½ pounds butternut squash - a small one
- 1 small head fresh garlic - for roasting
- Olive oil
- Salt and pepper
- ½ cup whole milk
For the mac and cheese:
- ¾ pound pasta shells
- 6 tablespoons unsalted butter
- 1 tablespoon all purpose flour
- 1 teaspoon garlic powder
- 1 very small pinch ground nutmeg
- ½ teaspoon fresh thyme leaves - minced
- ½ teaspoon fresh rosemary - minced
- 1 cup heavy cream
- ½ cup whole milk - plus more as needed
- 6 ounces freshly shredded yellow cheddar cheese - plus more for topping
- 6 ounces freshly shredded Gouda cheese - plus more for topping
- Salt and pepper - to taste
For the breadcrumb topping:
- ⅓ cup panko breadcrumbs
- 2 tablespoons unsalted butter
- ½ teaspoon minced rosemary - or 1 small sage leaf
Instructions
Make the butternut squash puree:
- Preheat oven to 400°F.
- Slice the top off the garlic head to expose the cloves. Drizzle with olive oil and season with salt and pepper. Wrap tightly in foil to seal. Set aside.
- Roast: Cut the butternut squash in half lengthwise and scoop out the seeds. Place it on a large baking sheet, flat side up. Drizzle with olive oil and season well with salt and pepper. Place the foil-wrapped garlic head on the pan. Roast at 400°F for 50 minutes, until very tender.
- Scoop out the squash from the skin (you should have about 1½ cups). Squeeze the roasted garlic from its skin.
- Blend the squash and garlic cloves with ½ cup milk until smooth and thick.
Make the mac and cheese:
- Reduce oven to 375°F.
- Meanwhile, cook the pasta until just shy of al dente (it will finish cooking in the oven). Reserve some pasta water, then drain.
- In a large 4-quart shallow Dutch oven braiser, melt butter over medium heat. Add flour and stir for 1 minute. Add garlic powder, nutmeg, thyme, and rosemary and cook for another 1-2 minutes to bloom the seasonings.
- Stir in the butternut squash puree. Then, gradually stir in the heavy cream and milk as needed, and bring to a low simmer.
- Reduce to low. Stir in the cheeses until melted and smooth, just a few seconds. Turn off the heat. Season with salt and pepper to taste.
- Stir in the cooked pasta. Add a splash of the reserved pasta water to loosen it up as needed.
Assemble and bake:
- Make the breadcrumb topping: In a pan, melt 2 tablespoons of butter and toss with the panko and herbs until it smells a little nutty.
- Transfer the mac and cheese to a 9×13 baking pan if needed (I baked it in the same Dutch oven braiser I used earlier). Top with more shredded cheese, followed by an even layer of the buttered breadcrumbs.
- Bake UNCOVERED at 375°F for 20-25 minutes, until bubbling and browned on top. Let cool slightly before serving. Serve warm.
Notes
- Use only one tablespoon of flour, as the thick squash puree acts as a natural thickener.
- Turn the heat to low before adding freshly shredded block cheese to prevent a grainy or oily sauce.
- Reserve starchy pasta water to loosen the thick sauce before baking.
- Use just a pinch of nutmeg. A little bit goes a long way. You can always add more to taste at the end.
- Make ahead: Roast and blend the squash up to 3 days in advance, or assemble the unbaked dish without breadcrumbs 1 day ahead.
- Storage: Keep leftovers in an airtight container in the fridge for 3 to 4 days.
- Freezing: Freeze baked portions for up to 3 months, thaw overnight in the fridge.
- Reheat at 350°F in the oven for larger portions, or in the microwave with a splash of milk for smaller portions.
- Stovetop: Skip the baking step and serve immediately for a creamy stovetop version.
- Swap the fresh squash for 1½ cups of canned butternut squash puree.
- Other cheeses: Gruyère, fontina, or white cheddar.
- Mix in crispy bacon, pancetta, or sautéed spinach.
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