Preheat the oven to 425 degrees.
Roast Butternut Squash: Add the butternut squash cubes to a 9x13-inch baking dish. Drizzle with oil and sprinkle with 1 teaspoon salt and ¼ teaspoon black pepper. Toss to coat and then roast in the preheated oven for 22-25 minutes, or until tender.
1 lb. butternut squash, 1 Tbsp. oil, 2 ½ tsp. salt, ½ tsp. black pepper
Puree Squash: Once roasted, add to a large high-speed blender or food processor along with 2 teaspoons of fresh herbs and nutmeg. Blend for 1-2 minutes, or until smooth and no clumps remain. Set aside until ready to use.
2 tsp. rosemary, ⅛ tsp. nutmeg
Boil Macaroni: Boil pasta in a large pot according to package directions. Drain in a colander and set aside. (Optional: drizzle a tablespoon of oil over the pasta and toss to combine to prevent it from clumping together while it cools.)
12 oz. pasta
Cook Bacon and Shallots: Add bacon pieces to a Dutch oven or large skillet over medium-high heat and cook for 7-8 minutes, or until crispy. Remove the bacon from the skillet using a slotted spoon and let drain on a paper towel-lined plate. Remove the bacon grease from the Dutch oven, wipe out any burnt bits, and pour back in 1 tablespoon of grease. Add the diced shallots and cook for 2-3 minutes, or until tender. Add the minced garlic and cook for 30 seconds, or until fragrant.
5 oz. bacon, 2 shallots, 2 cloves garlic
Make the Butternut Squash & Cheese Sauce: Whisk in flour until it thickens and forms a paste. Quickly pour in ½ cup broth, mixing to combine. Slowly add in the remaining broth and milk, ½ cup at a time, whisking well after each addition. Wait until the sauce thickens before pouring in the next amount. Add the cheese, pureed squash, and cooked pasta to the sauce. Stir until well combined.
¼ cup flour, 1 ½ cups broth, 1 ½ cups milk, 1 cup Cheddar cheese, 1 cup Gruyere cheese
Add Macaroni to Baking Dish: Pour the macaroni and cheese into the previously used 9x13-inch baking dish and top with the cooked bacon pieces. In a small bowl, toss together the melted butter, breadcrumbs, and Parmesan cheese. Sprinkle the topping over the pasta.
⅓ cup Panko breadcrumbs, ¼ cup Parmesan cheese, 1 Tbsp. butter
Bake in Oven: Reduce the oven temperature to 375 degrees and bake for 25-30 minutes, or until the topping begins to brown. (Optional: broil for an additional 1-2 minutes.) Let sit for 5-10 minutes so the sauce can thicken up and then serve with additional fresh herbs.