Creamy Baked Butternut Squash Mac and Cheese with Bacon

butternut squash Mac and cheese in the skillet to be served

5 from 4 votes

Creamy Baked Butternut Squash Mac and Cheese with Bacon

A cozy fall twist on classic mac and cheese, this Butternut Squash Mac and Cheese with Caramelized Onions and Bacon is creamy, golden, and full of comforting flavor. Made with real butternut squash, melted cheddar, and crisp bacon, it’s an easy, family-friendly baked dinner perfect for chilly evenings or holiday gatherings!

Prep Time25

Cook Time45

Resting10

Total Time1 20

Course: Main Course, Side Dish

Cuisine: American

Difficulty: Medium

Servings: generous portions

Calories: 520kcal

Author: Nora from Savory Nothings

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

Instructions

Prep: 
Grease a 9x13-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!

Notes

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.

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