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Doesn’t late autumn just call for something warm and golden? This Butternut Squash Mac and Cheese recipe is creamy and rich, with caramelized onions and bits of crisp bacon tucked into every bite. It’s the kind of meal that fills your kitchen with quiet comfort.
What’s to love
- Simple, honest ingredients. Everyday staples, nothing fussy – creamy sauce, real vegetables, and that quiet sweetness butternut squash brings.
- Make-ahead easy. Assemble earlier in the day, bake while the house winds down! Which makes it the perfect dish for Thanksgiving or other holiday dinners, too.
- The kind of leftovers that never last. Reheated, it’s even better — thick, cheesy, and soul-warming.
It’s simple food made from real ingredients, baked until bubbling and toasty on top. No perfection needed – just warmth, a steady oven, and a table to gather around!
Printable recipe
Ingredients
For the macaroni:
- 1 (12-oz) box elbow macaroni (or small shells)
- salt (for the pasta water)
For the bacon and onions:
- 1 tablespoon olive oil or butter
- 4 oz bacon (chopped)
- 1 large onion (thinly sliced)
For the sauce:
- ½ medium butternut squash (peeled, seeded, and diced (about 2 cups))
- ½ teaspoon salt
- ½ cup chicken stock
- 2 ½ cups whole milk (or a mix of milk and cream for extra richness)
- 1 pinch ground nutmeg
- freshly cracked black pepper
- 1 teaspoon Dijon mustard (optional, adds depth)
- ½ cup shredded mozzarella cheese
- 1 ½ cups sharp cheddar cheese
- ¼ cup grated Gruyère or Parmesan (optional but divine)
For the topping:
- 1 tablespoon butter
- ½ cup fresh breadcrumbs (or crushed butter crackers)
- 1 teaspoon fresh thyme or finely chopped sage leaves (optional)
Tips
- Cook the onions slowly. Don’t rush the caramelizing step – that 10–15 minutes over medium-low heat adds depth and sweetness to the whole dish.
- Blend the squash until completely smooth. A silky base makes the sauce taste rich and velvety, not grainy. If it looks too thick, whisk in a splash more milk.
- Use freshly shredded cheese. Pre-shredded cheeses contain anti-caking agents that can make the sauce less creamy – shredding your own melts more smoothly and gives a better texture.
- Optional cozy touches: Drizzle a little browned butter over the top before baking. Add a few sage leaves on top of the casserole as it bakes — they crisp great. Serve with roasted Brussels sprouts or a fall salad with apples and walnuts.
Instructions
- Prep: Grease a 9×13-inch baking dish and preheat oven to 375°F. Get your ingredients ready.
- Cook the pasta: Bring a large pot of salted water to a boil and cook the pasta until just al dente (about 1 minute less than package directions – this ensures it won’t overcook in the oven.) Drain and rinse under cool water to stop the cooking. Set aside.1 (12-oz) box elbow macaroni, salt
- Cook bacon and onions: In a large skillet, heat the oil or butter over medium heat. Add bacon and cook until starting to crisp. Stir in the onion and cook slowly over medium-low to medium heat for 10–15 minutes, stirring often, until golden and caramelized. Remove from heat and set aside.Tip: Keep the heat moderate and take your time with the onions. Stir often and let them turn deep golden – that slow caramelization is what builds the flavor foundation.1 tablespoon olive oil or butter, 4 oz bacon, 1 large onion
- Make the squash base: In a saucepan, combine the diced squash, chicken stock, and milk. Bring to a simmer, cover lightly, and cook for 15–20 minutes, until squash is very soft. Blend until smooth using an immersion blender or standard blender.Tip: If your squash cubes are on the larger side, add a few extra minutes to soften completely. After blending, the sauce should be as smooth as a bisque – no lumps.½ medium butternut squash, ½ teaspoon salt, ½ cup chicken stock, 2 ½ cups whole milk
- Finish the sauce: Over low heat. stir in nutmeg, pepper, and mustard (if using). Add the cheeses gradually, stirring until smooth and melty. Taste and adjust seasoning.Tip: Add the cheeses gradually over low heat, stirring between each addition to prevent curdling. If the sauce thickens too much, thin with a splash of warm milk.1 pinch ground nutmeg, freshly cracked black pepper, 1 teaspoon Dijon mustard, ½ cup shredded mozzarella cheese, 1 ½ cups sharp cheddar cheese, ¼ cup grated Gruyère or Parmesan
- Combine: Stir the pasta, caramelized onions and bacon into the sauce. Pour into the prepared baking dish (or into a cast iron skillet!)Tip: Taste the sauce before baking – it should be well-seasoned now, since the pasta will mellow it slightly.
- Make the topping: Melt butter in a small skillet, then stir in breadcrumbs (or crackers) and herbs until golden. Sprinkle evenly over the macaroni.Tip: If you’re using fresh breadcrumbs, toast them to pale gold before sprinkling – they’ll crisp up great without burning.½ cup fresh breadcrumbs, 1 tablespoon butter, 1 teaspoon fresh thyme or finely chopped sage leaves
- Bake: Bake for 20–25 minutes, until bubbling and golden on top. Let the dish rest 5–10 minutes after baking so the sauce can settle and cling to the pasta. It’s worth the wait!
Creamy Baked Butternut Squash Mac and Cheese with Bacon
make your kitchen smell like home?Butternut squash Mac and cheese FAQs
Yes, absolutely. Use about 1 ½ cups of purée and warm it gently with the milk before adding cheese. The flavor will be slightly mellower but still delicious.
Sharp cheddar is the classic base, but adding mozzarella or Gruyère makes the sauce extra silky. Shred your own cheese if possible – it melts more smoothly and creates a better texture.
Melt the cheese over low heat and add it gradually, stirring after each handful. High heat or too much cheese at once can cause the sauce to split or turn grainy.
Yes. Just skip the bacon and cook the onions in butter or olive oil instead. A sprinkle of smoked paprika adds a similar warmth.
Perfect to serve with
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Karen says
Thank you for sharing this recipe
Kristi CAll says
Could this be frozen for future use? Maybe not cook the pasta?
Nora says
Hi Kristi, I have honestly never tried freezing it. I know most pasta bakes can easily be fully assembled (with the pasta cooked) and then frozen (without the baking step). If you go ahead and try it, please let us know how it worked out for you – I’m sure it would help others!
Kelly says
I’m not a fan of squash but will this recipe hide that squash flavor fairly well?
Nora says
Hi Kelly, if you’re not a fan of squash I would honestly suggest looking for a different recipe. I know there’s lots of healthier mac and cheese recipes out there with cauliflower, perhaps that would be a better choice for you? Butternut squash has a very distinct flavor, so if you don’t like it I’m sure it will come through for you in this recipe. Hope that helps 🙂
Mary Nasvik says
The recipe sounds great, but what is a “rasher” of bacon? I make my mac n cheese with cooked and smashed cauliflower.
Nora says
Hi Mary, thanks for asking. A rasher is just a strip of thin-cut bacon. You can also use thick-cut bacon cut into small cubes. I’ve only made mac and cheese with cauliflower once so far, but it was delicious!
Annie says
Oh yes!! You know, I had never ever tried butternut squash until last year! Where have I been?! I love this lightened up version of a classic mac and cheese! We might just have it this week!
Nora says
You’ll need to catch up on the butternut squash eating front 😉 Thanks Annie!
Izzy says
I think I’ve always had a love for cheesy noodle casseroles! I just made a butternut squash mac n cheese and have been enjoying it for days now! This one is extra cheesy and looks amazing!
Nora says
There’s just something about carbs covered in cheese and butternut squash that’s so comforting. Thanks Izzy!
Rachel @ Bakerita says
I want this for dinner!! And you NAILED that cheesy stretch shot at the top 🙂 this looks amazing, Nora!
Nora says
Haha, I had to hush everyone out of the kitchen to leave me and my cheese in peace to photograph 😀 Thanks Rachel!
Denise | Sweet Peas & Saffron says
This is calling my name in a BIG big way! Love butternut, pasta, cheeeeese and bacon! All of the best things on this planet in one dish 🙂 🙂
Nora says
Exactly! 😀 Thanks so much for your sweet comment, Denise!
marcie says
I love how you lightened up mac ‘n cheese and made it perfect for fall, Nora! A little bacon does go a long way, and I’m sure it gave this such a nice flavor. This looks so cheesy and delicious!
Nora says
Thank you so much, Marcie!
Medha @ Whisk & Shout says
This looks absolutely unreal! So cheesy and delicious but so healthy. Pinning 🙂
Nora says
Thanks Medha!