The Ultimate Butternut Squash Mac and Cheese with Bacon and Apple

The first truly chilly evening of the season always calls for something special. It’s a craving for a meal that feels like a warm hug from the inside out. While classic mac and cheese is always a good idea, I want to share a recipe that takes that comfort to a whole new level. This Butternut Squash Mac and Cheese with Bacon and Apple is the answer. It’s a symphony of fall flavors, blending sweet roasted squash, deeply savory caramelized onions, smoky bacon, and a surprising pop of tart apple into an unforgettable dish.

This isn’t just another pasta recipe; it’s a culinary experience that’s surprisingly simple to create. Forget the boxed stuff. We’re building layers of flavor from scratch that will make you feel like a kitchen superstar. Trust me, you’ve got this.

Quick Recipe

• Preparation Time: 30M
• Cooking Time: 1H
• Total Time: 1H30M
• Type of dish: Main Course
• Cuisine: American
• Recipe Yield: 6-8 servings
• Calories: 575 calories per serving

Recipe Highlights

Feature	Why You’ll Love It
Incredible Flavor	The combination of sweet, savory, smoky, and tart creates a perfectly balanced and deeply satisfying meal.
Extra Creamy & Nutritious	The butternut squash puree creates a velvety smooth sauce, adding nutrients and creaminess with less cheese.
A True Showstopper	This is the ultimate fall comfort food, perfect for a cozy family dinner or impressing guests at a holiday gathering.
Make-Ahead Friendly	You can assemble the entire dish ahead of time and bake it just before serving. Perfect for busy days!

Why This Recipe Just Works

You might be wondering if all these ingredients really belong together in mac and cheese. The answer is a resounding YES! I’ve made this dozens of times, and the magic is in the balance.

• The Butternut Squash: We roast the squash first, which is a crucial step. Roasting concentrates its natural sugars and brings out a nutty sweetness that you just can’t get from boiling. It becomes the base of our incredibly creamy sauce.
• The Caramelized Onions: This is where we build our deep, savory foundation. Taking the time to slowly caramelize the onions transforms them from sharp and pungent to sweet and jammy. It’s a key component of our caramelized onion mac and cheese.
• The Bacon: It adds that salty, smoky crunch that cuts through the richness of the cheese sauce. We even use a little of the rendered bacon fat to start our sauce for an extra layer of flavor.
• The Apple: This is my secret weapon! A crisp, tart apple like a Granny Smith provides a bright, acidic note that prevents the dish from feeling too heavy. It’s a surprising but delightful contrast.

Together, these elements create a sophisticated, grown-up version of a childhood classic that will have everyone asking for seconds.

Gather Your Ingredients

Think of this list as your cast of characters, each playing a vital role.

• For the Main Event:
  • Pasta: 1 pound (454g) of short pasta like cavatappi, shells, or elbow macaroni. Choose a shape with plenty of nooks and crannies to hold the sauce.
  • Butternut Squash: 1 medium (about 2-3 pounds) butternut squash, peeled, seeded, and cut into 1-inch cubes.
  • Bacon: 8 slices of thick-cut bacon, chopped.
  • Apple: 1 large tart apple (like Granny Smith), cored and diced into small ½-inch pieces.
  • Onion: 1 large yellow onion, thinly sliced.
• For the Creamy Cheese Sauce:
  • Butter: 4 tablespoons, unsalted. You may need less depending on how much fat your bacon renders.
  • All-Purpose Flour: ¼ cup. This is what thickens our sauce.
  • Whole Milk: 3 cups, warmed. Using warm milk helps the sauce come together smoothly without lumps.
  • Cheese: 3 cups (12 oz) shredded cheese. I recommend a mix of 1 ½ cups Gruyère (for melting and nutty flavor) and 1 ½ cups sharp cheddar (for that classic tangy mac and cheese taste).
  • Spices: ½ teaspoon smoked paprika, ¼ teaspoon grated nutmeg, salt, and freshly ground black pepper to taste.
• For the Topping (Optional but Recommended):
  • Panko Breadcrumbs: ½ cup for a super crispy topping.
  • Reserved Bacon: The crispiest bits you saved.
  • Fresh Thyme: A few sprigs for garnish.

Essential Tools for Mac and Cheese Magic

You don’t need anything too fancy, just a few kitchen basics:

• Large pot or Dutch oven
• Baking sheet
• Large skillet
• Blender (a standard or immersion blender works great)
• 9×13-inch baking dish

Step-by-Step: Let’s Make Butternut Squash Mac and Cheese

Take a deep breath. We’re going to break this down into simple, manageable steps. Put on some good music and let’s get cooking!

Step 1: Roast the Squash and Cook the Pasta

• First things first, preheat your oven to 400°F (200°C).
• Toss your cubed butternut squash with a tablespoon of olive oil, a pinch of salt, and pepper right on a baking sheet. Spread it in a single layer and roast for 20-25 minutes, or until it’s fork-tender and lightly caramelized. This deepens the flavor wonderfully.
• While the squash roasts, bring a large pot of salted water to a boil and cook your pasta according to package directions until al dente. This is important! The pasta will continue to cook in the oven, and you want it to have a slight bite. Drain and set aside.

Step 2: Cook the Bacon and Caramelize the Onions

• In a large skillet or Dutch oven over medium heat, cook the chopped bacon until it’s nice and crispy. Use a slotted spoon to transfer the bacon to a paper towel-lined plate, but leave about 2 tablespoons of the rendered fat in the skillet. This fat is liquid gold!
• Add the sliced onions to the same skillet with the bacon fat. Turn the heat down to medium-low and cook slowly for 20-25 minutes, stirring occasionally. Be patient here. You want them to become a deep golden brown, soft, and sweet. Don’t rush this step; it’s where so much of the flavor is built for our caramelized onion mac and cheese.

Step 3: Build the Creamy Squash and Cheese Sauce

• Once the onions are caramelized, add 2-3 tablespoons of butter to the skillet and let it melt. Whisk in the ¼ cup of flour and cook for about one minute, stirring constantly. This little paste is called a “roux,” and it’s what will thicken our sauce.
• Slowly stream in the warm milk, whisking continuously to prevent any lumps from forming. Continue to cook, stirring, until the sauce thickens enough to coat the back of a spoon (about 5-7 minutes).
• Now, turn the heat down to low. Add the roasted butternut squash to the sauce. Using an immersion blender, blend directly in the pot until the sauce is completely smooth and velvety. If you don’t have an immersion blender, carefully transfer the sauce and squash to a standard blender and blend until smooth, then return it to the pot. This is how we create that signature creamy squash pasta texture.
• Remove the pot from the heat and stir in the shredded cheeses, smoked paprika, and nutmeg. Stir until the cheese is fully melted and the sauce is glorious. Season with salt and pepper to your liking.

Step 4: Assemble and Bake to Perfection

It’s time to bring it all together! To your pot of cheese sauce, add the cooked pasta, the caramelized onions, the diced apple, and about two-thirds of the crispy bacon. Stir gently until everything is lovingly coated in that beautiful orange sauce.

Pour the mixture into your 9×13-inch baking dish. In a small bowl, toss the panko breadcrumbs with a drizzle of olive oil or melted butter. Sprinkle the breadcrumbs evenly over the top of the mac and cheese, followed by the remaining crispy bacon.

Bake for 15-20 minutes, or until the sauce is bubbly and the topping is golden brown and crisp.

A New Fall Favorite

Let the mac and cheese rest for a few minutes before serving—this helps the sauce set up. Garnish with some fresh thyme and get ready for rave reviews. This Butternut Squash Mac and Cheese with Bacon and Apple is more than just a meal; it’s an event. It’s the perfect dish to have in your back pocket for cozy nights, holiday potlucks, and any time you need a little extra comfort.

I hope you and your family love this recipe as much as mine does. Happy cooking!

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