If you’re craving a cozy, comforting dish that dazzles with a clever twist, this Butternut Squash Mac and Cheese with Bacon Recipe is exactly what you need. Silky roasted butternut squash creates a velvety cheese sauce that’s both luscious and subtly sweet, perfectly balanced by crispy, savory bacon bits. Every bite is a warm hug of creamy, cheesy goodness with just the right touch of herbaceous flavor and a crispy breadcrumb topping that makes this mac and cheese an unforgettable crowd-pleaser.

Ingredients You’ll Need
Gathering simple, wholesome ingredients is the secret to bringing together this dish’s incredible flavors and textures. Each component plays a starring role, from the tender butternut squash that enriches the sauce to the crispy bacon that adds a smoky crunch. Let’s break down exactly what you’ll need to make this magical mac and cheese.
- 1 pound butternut squash, peeled and cubed: Roasting it brings out its natural sweetness and creates a creamy base for the sauce.
- 1 tablespoon oil (olive or avocado): For roasting the squash to a tender perfection without sticking.
- 2 ½ teaspoons salt (divided): Essential for seasoning every layer of this dish.
- ½ teaspoon black pepper (divided): Adds a subtle kick and balances the sweetness.
- 2 teaspoons fresh herbs (rosemary, sage, and/or thyme, finely chopped): Herbaceous notes that brighten up the richness.
- ⅛ teaspoon ground nutmeg: A hint of warmth and depth that marries beautifully with the cheese.
- 12 ounces pasta (elbows, gluten-free if needed): The perfect vehicle for soaking up all that cheesy sauce.
- 5 ounces bacon, cut into pieces: Crispy, smoky contrast that adds incredible flavor.
- 2 shallots, finely chopped: Mild and sweet, they provide an aromatic base.
- 2 cloves garlic, minced: Brings fragrant, savory depth to the dish.
- ¼ cup flour (all-purpose or gluten-free blend): Thickens the cheese sauce to luscious perfection.
- 1 ½ cups broth (chicken or vegetable, divided): Adds flavor and helps build the sauce’s creamy texture.
- 1 ½ cups milk (regular or plant-based): Keeps the sauce smooth and rich.
- 1 cup Cheddar cheese, shredded: Sharp and melty, it’s classic mac and cheese goodness.
- 1 cup Gruyere cheese, shredded: Adds nuttiness and a beautiful melt.
- ⅓ cup Panko breadcrumbs (gluten-free if needed): For that irresistible crunchy topping.
- ¼ cup grated Parmesan cheese: Adds salty, umami richness on top.
- 1 tablespoon butter: Binds the topping ingredients and enhances flavor.
How to Make Butternut Squash Mac and Cheese with Bacon Recipe
Step 1: Roasting the Butternut Squash
Start by preheating your oven to 425 degrees. Toss your butternut squash cubes with oil, a sprinkle of salt, and pepper, then spread them out in a baking dish. Roasting caramelizes the squash’s natural sugars, making it tender and sweet—the very heart of your cheese sauce.
Step 2: Blending the Squash
Once roasted to a tender, golden perfection, the squash gets blended smooth with fresh herbs and a touch of nutmeg. This puree transforms into a creamy, flavorful base that elevates the whole mac and cheese beyond the ordinary.
Step 3: Cooking the Pasta
While the squash roasts and cools slightly, cook your pasta until just tender. Draining and tossing it with a bit of oil keeps it from sticking, so it melds beautifully with the sauce later without clumping.
Step 4: Crisping Bacon and Sautéing Aromatics
Cook the bacon until crispy to add that smoky crunch everyone loves. Then, using the rendered bacon fat, sauté shallots and garlic until fragrant and tender—layering in that wonderful savory depth before the sauce-making begins.
Step 5: Making the Cheese Sauce
Stir flour into the bacon and aromatics mixture creating a thick paste, then gradually whisk in broth and milk, letting the sauce thicken slowly with each addition. This patient process delivers a perfectly smooth and luscious base that is then enriched with shredded cheeses and the pureed squash. Mixing in the cooked pasta ensures every bite is loaded with creamy goodness.
Step 6: Assembling and Baking
Pour your cheesy macaroni into the baking dish, scatter the crispy bacon on top, then sprinkle with a buttery mix of Panko breadcrumbs and Parmesan. Baking at 375 degrees crisps the topping to a golden brown, adding the perfect textural contrast to the creamy pasta underneath. A quick broil can add an extra touch of color if you like!
How to Serve Butternut Squash Mac and Cheese with Bacon Recipe
Garnishes
Fresh herbs like thyme or rosemary sprinkled on top after baking give this dish not only a pop of color but also a burst of fresh, aromatic flavor that complements the richness beautifully. A few grinds of black pepper or a light drizzle of olive oil can also elevate the presentation and taste.
Side Dishes
This Butternut Squash Mac and Cheese with Bacon Recipe pairs wonderfully with crisp green salads, roasted Brussels sprouts, or steamed broccoli to add fresh and bright contrast to the creamy, indulgent pasta. If you want to stick with comfort food vibes, some soft dinner rolls or garlic bread are always a perfect match.
Creative Ways to Present
For a fun twist, try serving individual portions in ramekins topped with extra crispy bacon and breadcrumbs. Or turn it into a layered casserole with alternating layers of mac and cheese and caramelized onions or sautéed mushrooms for added earthiness. The golden crust and creamy interior can even be scooped into hollowed-out mini pumpkins for an impressive autumnal presentation.
Make Ahead and Storage
Storing Leftovers
This dish keeps beautifully in the fridge for up to 3 days. Store the leftovers in an airtight container to maintain moisture and freshness. The flavors often deepen overnight, making for an even better next-day meal.
Freezing
If you want to freeze your Butternut Squash Mac and Cheese with Bacon Recipe, wait until it’s completely cooled, then pack it tightly in a freezer-safe container. It will keep well for up to 2 months. Thaw overnight in the fridge before reheating to keep the texture just right.
Reheating
Reheat leftovers gently in the oven at 350 degrees, covered with foil to prevent drying out, for about 20 minutes or until warmed through. You can also microwave individual servings, but stirring occasionally will help maintain that creamy texture.
FAQs
Can I make this Butternut Squash Mac and Cheese with Bacon Recipe vegetarian?
Absolutely! Simply omit the bacon and use vegetable broth. You can add extra herbs or sautéed mushrooms to boost the savory flavors. Adding smoked paprika can also mimic that smoky depth bacon provides.
What type of pasta works best for this recipe?
Classic elbow macaroni is traditional and works wonderfully here because its shape catches the sauce perfectly. However, feel free to use gluten-free pasta if preferred, or shapes like shells or cavatappi for added texture.
Can I substitute the cheeses?
Yes, the combination of Cheddar and Gruyere is ideal for melt and flavor. But you can swap Gruyere for mozzarella or fontina, and Cheddar for Colby or even a sharp Monterey Jack depending on your taste and what you have on hand.
Is this recipe suitable for meal prep?
Definitely! The Butternut Squash Mac and Cheese with Bacon Recipe reheats beautifully, making it a perfect make-ahead meal for busy weeks. Just portion out and refrigerate or freeze for convenient comfort food whenever you need it.
How do I make the breadcrumb topping extra crispy?
Using Panko breadcrumbs and mixing them with melted butter and Parmesan cheese ensures a crisp top. For an even crunchier finish, broil the dish for 1-2 minutes after baking—just watch carefully to avoid burning!
Final Thoughts
Whether you’re cooking for a cozy family dinner or looking to impress friends with something a little different, this Butternut Squash Mac and Cheese with Bacon Recipe is a true winner. It combines comforting tradition with seasonal flair, creating a dish that’s hearty, flavorful, and downright irresistible. Give it a try—you might just find your new favorite mac and cheese in this vibrant, cozy bowl.
Print
Butternut Squash Mac and Cheese with Bacon Recipe
- Prep Time: 20 minutes
- Cook Time: 55 minutes
- Total Time: 1 hour 15 minutes
- Yield: 8 servings
- Category: Main Dish
- Method: Baking
- Cuisine: American
Description
This Butternut Squash Mac and Cheese with Bacon is a comforting twist on the classic favorite, featuring a creamy, flavorful butternut squash cheese sauce combined with crispy bacon and topped with a crunchy breadcrumb and Parmesan crust. Perfectly roasted squash adds natural sweetness and depth to the sauce, while the blend of cheddar and Gruyere cheeses provides rich, melty goodness. Ideal for cozy family dinners, this dish is satisfying and packed with flavor.
Ingredients
Roasted Butternut Squash
- 1 pound butternut squash, peeled and cut into ½ to 1-inch cubes
- 1 tablespoon oil (olive or avocado)
- 2 ½ teaspoons salt, divided
- ½ teaspoon black pepper, divided
- 2 teaspoons fresh herbs (rosemary, sage, and/or thyme), finely chopped
- ⅛ teaspoon ground nutmeg
Pasta
- 12 ounces pasta (elbows, gluten-free if needed)
Bacon and Aromatics
- 5 ounces bacon, cut into ½-inch pieces
- 2 shallots, finely chopped
- 2 cloves garlic, finely minced
Cheese Sauce
- ¼ cup all-purpose flour (or gluten-free 1-to-1 blend)
- 1 ½ cups broth (chicken or vegetable), divided
- 1 ½ cups milk (regular or plant-based)
- 1 cup shredded Cheddar cheese
- 1 cup shredded Gruyere cheese
Topping
- ⅓ cup Panko breadcrumbs (gluten-free if needed)
- ¼ cup grated Parmesan cheese
- 1 tablespoon butter
Instructions
- Preheat Oven: Preheat your oven to 425 degrees Fahrenheit to prepare for roasting the butternut squash.
- Roast Butternut Squash: Place the diced butternut squash in a 9×13-inch baking dish. Drizzle with oil, sprinkle with 1 teaspoon salt and ¼ teaspoon black pepper, and toss to coat evenly. Roast in the preheated oven for 22-25 minutes or until the squash is tender when pierced with a fork.
- Puree Squash: Transfer the roasted squash to a high-speed blender or food processor. Add the finely chopped fresh herbs and ground nutmeg. Blend for 1-2 minutes until completely smooth with no lumps. Set this puree aside to use in your sauce later.
- Cook Pasta: Bring a large pot of salted water to a boil and cook the pasta according to package instructions until al dente. Drain the pasta in a colander and optionally toss with a tablespoon of oil to prevent sticking. Set aside.
- Cook Bacon and Shallots: In a Dutch oven or large skillet over medium-high heat, cook the bacon pieces for 7-8 minutes until crispy. Remove bacon with a slotted spoon and drain on paper towels. Carefully pour off excess bacon grease leaving about 1 tablespoon in the pan. Add the chopped shallots to the pan and sauté for 2-3 minutes until tender. Add the minced garlic and cook for an additional 30 seconds until fragrant.
- Make Cheese Sauce Base: Whisk in the flour to the bacon and shallot mixture to form a thick paste. Gradually pour in ½ cup of the broth while whisking to combine smoothly. Slowly add the remaining broth and milk, about ½ cup at a time, whisking well after each addition. Continue stirring until the sauce thickens to a creamy consistency.
- Combine Sauce with Squash and Pasta: Stir in the shredded Cheddar and Gruyere cheeses until melted and smooth. Add the pureed butternut squash and cooked pasta to the sauce, folding together until everything is evenly incorporated.
- Assemble in Baking Dish: Pour the macaroni and cheese mixture into the same 9×13-inch baking dish previously used for roasting the squash. Sprinkle the crispy bacon pieces evenly over the top. In a small bowl, mix melted butter with the Panko breadcrumbs and grated Parmesan cheese, then scatter this topping over the pasta.
- Bake and Finish: Reduce the oven temperature to 375 degrees Fahrenheit and bake for 25-30 minutes until the topping is golden brown and crisp. For an extra crunchy topping, broil for 1-2 minutes at the end if desired. Let the dish rest for 5-10 minutes to thicken the sauce before serving. Garnish with extra fresh herbs if preferred.
Notes
- Use gluten-free pasta, flour, and breadcrumbs to make this recipe gluten-free.
- Plant-based milk and vegetable broth make this dish vegetarian (omit bacon or substitute with plant-based alternatives).
- Fresh herbs can be substituted based on availability; thyme, rosemary, and sage all work well.
- Broiling at the end helps achieve a more golden and crunchy topping but watch carefully to avoid burning.
- Leftovers can be stored in the refrigerator for up to 3 days and reheated in the oven for best texture.

