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close-up of baked butternut squash mac and cheese in orange bowl

Baked Butternut Squash Mac and Cheese

Loaded with butternut squash, Brussels sprouts, cheese and prosciutto, this baked butternut squash mac n cheese is a unique take on a traditional meal.
Course Pasta
Cuisine Italian
Prep Time 15 minutes
Cook Time 1 hour
Total Time 1 hour 15 minutes
Servings 12
Calories 362kcal
Author Ryan Beck


  • 1 lb elbow macaroni ( I used fall zucchette pasta from Trader Joe's)
  • 1 small butternut squash (4-5 cups cubed)
  • 3 cups Brussels sprouts, sliced thin into shreds
  • 2 tbsp olive oil
  • kosher salt and black pepper
  • 6 tbsp unsalted butter, divided
  • 2 tbsp fresh sage, chopped
  • ¾ cup panko breadcrumbs
  • ¼ cup shredded Parmesan cheese
  • 1 medium shallot, chopped
  • 3 tbsp all-purpose flour
  • 2 ½ cups milk, divided
  • pinch of nutmeg
  • 2 cups shredded sharp cheddar cheese
  • 4 oz prosciutto, julienned


  • Preheat oven to 400°F. Peel, seed and chop the butternut squash in 1" cubes. Place butternut squash chunks on baking sheet. Drizzle 1 tbsp olive oil and sprinkle with salt and pepper. Place the Brussels sprouts on a separate baking sheet and toss with 1 tbsp olive oil and a pinch of salt. Roast for 20-30 minutes or until tender. You might need to pull Brussels sprouts out early if they are browning. Once done reduce heat to 350°F.
  • Melt 2 tbsp butter in small pan over low heat. Once melted, add panko, sage and Parmesan and toss to combine. Set aside.
  • When butternut squash is done, add to blender with ½ cup milk and puree until smooth.
  • Heat 4 tbsp butter in large skillet over medium heat. Add shallots and cook for about 2 minutes or until translucent. Add flour and nutmeg and whisk until smooth and mixture starts to bubble. (About 2 minutes) While stirring, gradually add 2 cups milk and continue whisking until the sauce is creamy. Simmer the sauce for about 10 minutes until it thickens and you can coat the back of the spoon.
  • After sauce has thickened, add butternut squash mixture, cheddar cheese, prosciutto and Brussels sprouts and stir until combined. Remove from heat and set aside.
  • While sauce is cooking bring a large pot of water to a boil. Boil the pasta according to instructions. Grease a 11x7 inch baking dish and add the drained pasta and sauce. Mix thoroughly, making sure all the pasta is coated. Top with bread crumb mixture.
  • Bake for 20-25 minutes at 350°F or until breadcrumb mixture starts to brown. Serve immediately.


  • Try to be consistent when dicing your butternut squash so it cooks at the same time. If you have larger cubes of butternut squash, it will take longer to cook which just delays you in getting to eat. You can also save time by buying pre-cut butternut squash.
  • Use a food processor to shred your Brussels sprouts. It will save you 5-10 minutes in slicing the Brussels sprouts.
  • When cooking the pasta, boil it until it is al dente as the pasta will continue to cook in the oven.
  • Buy blocks of cheddar cheese and Parmesan cheese and shred it yourself. Pre-shredded cheese just doesn't taste the same. Plus pre-shredded Parmesan cheese has wood pulp in it!
  • When cooking the flour in the butter, stir constantly in a figure-eight motion with a wooden spoon for even cooking. You'll know the roux is ready for the milk when the butter/flour mixture has puffed slightly, about 2 minutes.
  • When adding milk to the roux, slowly add the milk a little at a time, whisking until smooth between each addition, until the roux forms a thin paste, then whisking in the remaining milk and bringing the mixture to a simmer. 
  • Skip the prosciutto if you are vegetarian but if you aren't, I highly recommend keeping it as it gives the mac and cheese a great salty bite.


Serving: 1serving | Calories: 362kcal | Carbohydrates: 34g | Protein: 16g | Fat: 18g | Saturated Fat: 9g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 5g | Trans Fat: 0g | Cholesterol: 45mg | Sodium: 603mg | Potassium: 321mg | Fiber: 3g | Sugar: 4g | Vitamin A: 2150IU | Vitamin C: 37.1mg | Calcium: 280mg | Iron: 1.4mg