Okay, so I messed this butternut squash mac and cheese recipe up twice before getting it right. First time, the sauce split and looked like orange cottage cheese – gross. Second time, I forgot to season it properly and my husband took one bite and was like “This tastes like baby food.” Ouch.

But here’s the thing – everyone keeps asking me for this creamy butternut squash mac and cheese recipe now, so I guess the third time really was the charm. And honestly? I’m kinda obsessed with it now. It’s become my go-to fall comfort food dish.

I think I originally got inspired by some fancy restaurant version… or maybe it was Pinterest? Honestly can’t remember anymore. But what I DO remember is being determined to make a healthy mac and cheese that didn’t taste like cardboard health food. Mission accomplished.

Why This Butternut Squash Mac and Cheese Actually Works :

Look, I’m gonna be honest – most “healthy” mac and cheese recipes are disappointing. You know the ones. They promise all the creamy goodness but deliver sad, watery noodles with no soul.

This creamy butternut squash mac and cheese is different. The butternut squash doesn’t just add nutrition (though hello, vitamin A!), it creates this naturally creamy, slightly sweet base that makes the whole dish feel indulgent. My 12-year-old doesn’t even know there are vegetables in it, which is saying something because that kid can spot a hidden veggie from a mile away.

And here’s something weird – the roasted butternut squash actually makes the cheese sauce MORE flavorful, not less. I discovered this by accident when I had leftover roasted squash in my fridge and thought “eh, why not throw it in?” Best kitchen mistake ever.

The key is—oh wait, I forgot to mention—you need to roast the squash first. Don’t try to shortcut this with frozen or pre-cut stuff. Trust me on this one.

What You’ll Need for the Best Butternut Squash Mac and Cheese :

Shopping for this can be… interesting. Good luck finding a decent butternut squash this time of year if you’re reading this in summer. But when it’s fall? Pure gold.

For the Pasta & Base:

1 pound elbow macaroni (or shells, or whatever pasta shape makes you happy)
2 pounds butternut squash, peeled and cubed (yeah, I know, peeling squash is annoying)
2 tablespoons olive oil
Salt and pepper (sea salt if you’re fancy, regular salt if you’re normal like me)

For the Cheese Sauce:

3 tablespoons butter (real butter, not the fake stuff)
3 tablespoons all-purpose flour
2½ cups whole milk (don’t even think about skim milk here)
8 oz sharp cheddar cheese, freshly grated (DO NOT buy pre-shredded cheese. Just don’t. It’s gross and doesn’t melt right)
4 oz Gruyere cheese, grated (or more cheddar if Gruyere is too fancy/expensive)
½ teaspoon nutmeg (this is what makes it taste like fall in a bowl)
1 teaspoon garlic powder
Salt and white pepper to taste

For the Topping:

1 cup panko breadcrumbs
2 tablespoons butter, melted
¼ cup grated Parmesan

How to Make Creamy Butternut Squash Mac and Cheese :

Preheat your oven to 425°F. And actually preheat it – don’t be like me and throw everything in a cold oven because you’re impatient.

Step 1: Roast the Butternut Squash
Toss those squash cubes with olive oil, salt, and pepper. Spread them on a baking sheet – don’t overcrowd or they’ll steam instead of roast. Nobody wants steamed squash in their mac and cheese.

Roast for about 25-30 minutes until they’re tender and slightly caramelized. Set timer for 25 minutes, then inevitably forget and panic at 35. It’s fine if they get a little dark – that’s extra flavor.

Step 2: Cook the Pasta
Cook your pasta according to package directions, but stop it one minute short of al dente. It’ll finish cooking in the oven. Drain and set aside. Do NOT rinse it – we want that starchy goodness.

Step 3: Make the Magic Sauce
This is where things get tricky. In a large saucepan, melt the butter over medium heat. Whisk in the flour and cook for about 2 minutes – you want to get rid of that raw flour taste but don’t let it brown.

Slowly – and I mean SLOWLY – whisk in the milk. Like, a splash at a time at first. If you dump it all in at once, you’ll get lumps and nobody wants lumpy mac and cheese. Been there, done that, learned the hard way.

Once it’s smooth and starting to thicken (about 5 minutes), add your roasted butternut squash. Here’s where I use my immersion blender to puree everything together until it’s creamy. You could use a regular blender, but be careful – hot liquids and blenders can be dangerous.

Step 4: Add the Cheese
Remove from heat and stir in the cheeses, nutmeg, garlic powder, salt, and pepper. Taste it – this is important. It should taste like fall had a baby with comfort food. Adjust seasoning as needed.

Step 5: Combine Everything
Mix the pasta with the butternut squash cheese sauce. It’ll look like a lot of sauce, but trust the process. Pour everything into a greased 9×13 baking dish.

Step 6: The Crispy Top
Mix panko, melted butter, and Parmesan. Sprinkle over the top. This is what separates good mac and cheese from GREAT mac and cheese.

Step 7: Bake
Bake at 375°F (yes, lower the temp) for 25-30 minutes until bubbly and golden on top. Let it rest for 10 minutes before serving – I know it’s torture, but it needs time to set up.

Pro Tips That Actually Matter

About the squash: Don’t skip roasting it. I tried using just steamed squash once and it was flavorless and watery. The roasting concentrates the flavors and adds that slightly caramelized sweetness.

Cheese grating: Seriously, grate your own cheese. Pre-shredded cheese has anti-caking agents that prevent smooth melting. Found this out by accident when comparing two batches side by side.

The nutmeg trick: My neighbor Sarah swears by this – she adds a tiny pinch of cayenne with the nutmeg. Not enough to make it spicy, just enough to wake up all the other flavors.

Make-ahead magic: You can assemble this butternut squash mac and cheese completely and refrigerate for up to 2 days before baking. Just add an extra 10 minutes to the baking time if it’s going in cold.

What Makes This Different from Regular Mac and Cheese :

The butternut squash doesn’t just hide in this recipe – it transforms it. You get this gorgeous golden color that screams “autumn comfort food,” plus the natural sweetness plays perfectly with the sharp cheddar.

It’s also way more nutritious than regular mac and cheese without tasting like diet food. The squash adds fiber, vitamins, and makes the whole dish more filling. My kids eat this and actually get vegetables without knowing it. Parent win.

And here’s something I discovered – leftovers are AMAZING. Like, better-than-the-first-day amazing. The flavors meld together overnight and it reheats beautifully in the oven.

Serving This Butternut Squash Mac and Cheese :

This is perfect as a side dish for Thanksgiving (hello, orange theme!), but honestly it’s hearty enough to be dinner on its own. I usually serve it with a simple green salad and call it a meal.

Kids eat this plain, adults like it with a sprinkle of fresh sage or chives. My husband adds hot sauce to everything, so he does that too. Whatever makes people happy.

It’s also amazing alongside roasted chicken or pork tenderloin. Last Sunday I made it with some herb-crusted pork and everyone was asking for seconds.

Storage and Leftovers :

Leftovers keep in the fridge for about 4 days. Reheat in the oven at 350°F until warmed through – usually about 20 minutes covered with foil. The microwave works in a pinch, but the oven keeps it from getting weird and rubbery.

You can also freeze portions in individual containers for up to 3 months. Great for those nights when you need comfort food but don’t want to cook.

Actually, you know what? I just remembered – my mom always said the best mac and cheese gets better the next day. She was right about this one.

Why This Recipe Works Every Time :

The secret is in the butternut squash puree creating this naturally creamy base that doesn’t break or get grainy like traditional cheese sauces sometimes do. The squash acts as a stabilizer while adding flavor and nutrition.

Plus, roasting the squash first concentrates all those fall flavors. It’s like autumn decided to move into your mac and cheese permanently.

If I can make this without turning it into orange soup (which I definitely did the first time), anyone can. It’s become one of those recipes I make when I want to feel like a kitchen genius without actually being one.

Come over sometime and I’ll make it for you – it’s even better shared with friends! 🧡