Butternut Squash Shells and Cheese Skillet Recipe

I absolutely love how this Butternut Squash Shells and Cheese Skillet Recipe brings together cozy fall flavors with a cheesy, creamy goodness that just hugs you from the inside out. It’s the kind of dish that feels like a warm hug on a chilly evening, yet it’s surprisingly fresh and light enough to enjoy any time you crave comfort food without the heaviness.

When I first tried this recipe, I was amazed by how the natural sweetness of the butternut squash perfectly balances the savory cheeses, making every bite rich but never overwhelming. You’ll find that it’s perfect for weeknight dinners or when you want something special but fuss-free. Trust me, once you make it, this skillet will become your go-to when you want something delicious, nutritious, and easy to pull together.

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Ingredients You’ll Need

This recipe uses simple, wholesome ingredients that complement each other beautifully to create a creamy, cheesy sauce with a subtle sweetness from fresh butternut squash. Make sure to choose fresh squash and good quality cheeses for the best results.

• Whole wheat pasta shells: Their cup-like shape holds onto the sauce perfectly, making every forkful extra cheesy.
• Butternut squash: The star of the dish; choose a firm, unblemished one for sweetness and smooth texture.
• Olive oil: Adds a lovely richness when cooking the squash before blending it into the sauce.
• Salt and pepper: Essential for balancing and enhancing all the flavors.
• Nutmeg: A tiny pinch adds warmth and depth—don’t skip it!
• Low-sodium chicken or vegetable stock: Helps cook the squash and adds savory depth without overpowering.
• Skim milk or unsweetened almond/coconut milk: For creamy smoothness; I like almond milk for a dairy-free twist.
• Fontina cheese: Melts beautifully and gives a silky texture to the sauce.
• Parmesan cheese: Adds sharpness and complexity; freshly grated gives the best flavor.
• Unsalted brown butter: Adds a nutty, caramelized richness that takes this recipe to the next level.
• Fine breadcrumbs: For that irresistible crunchy topping after baking.
• Fresh chopped herbs (sage, basil, cilantro, thyme): Brighten the dish with fresh herbal notes—you can’t go wrong here.

Variations

I love playing around with this Butternut Squash Shells and Cheese Skillet Recipe depending on the season or what’s in my fridge. Feel free to swap cheeses, add veggies, or even make it vegan-friendly with a few smart substitutions.

• Cheese swap: I once replaced fontina with gouda for a smoky twist that blew my mind—give it a try!
• Added greens: Stirring in sautéed kale or spinach just before baking adds color and nutrients without overwhelming the dish.
• Make it vegan: Use plant-based cheeses and coconut milk, and brown some vegan butter or olive oil instead of brown butter.
• Spice it up: Adding a pinch of cayenne or smoked paprika gives a fun kick if you enjoy a little heat.

How to Make Butternut Squash Shells and Cheese Skillet Recipe

Step 1: Prepare the Pasta and Butternut Squash

Start by preheating your oven to 375°F so it’s ready when you need it. Bring a large pot of salted water to a boil and cook the whole wheat pasta shells according to package instructions—usually about 8-10 minutes—until al dente. Drain and set aside.

Meanwhile, heat your cast-iron or oven-safe skillet over medium-low heat and add the olive oil. Toss in your butternut squash cubes seasoned with salt, pepper, and a pinch of nutmeg. Pour in the chicken or vegetable stock, cover the skillet, and let it simmer gently for 15-20 minutes. Keep stirring occasionally so the squash cooks evenly and doesn’t stick. You’ll know it’s done when it’s tender enough to mash smoothly.

Step 2: Make the Creamy Squash Cheese Sauce

Once the squash is tender, remove the cover and lower the heat to low. Use a potato masher or two forks to mash the squash right in the skillet, smoothing out all the chunks with the back of a spoon. Then stir in the milk, about 4 ounces of grated fontina cheese, and all of the parmesan. Keep stirring the mixture gently for about 5 minutes until the cheese melts and everything becomes silky smooth.

If the sauce feels a little thick or starchy, slowly add more milk a quarter cup at a time until it reaches a creamy consistency that will nicely coat the pasta. Lastly, stir in the brown butter — it adds a rich, nutty flavor that I learned makes this dish extra special. Taste and add more salt or pepper if needed.

Step 3: Combine, Top, and Bake

Fold the cooked pasta shells gently into the squash cheese sauce, taking a few minutes to toss everything until the shells are well coated. This is where the magic happens—you want every shell bursting with creamy flavor.

Sprinkle the remaining fontina cheese over the top, then add the breadcrumbs for a delightful crunchy layer. Pop the skillet into your preheated oven and bake for about 15 minutes, until you see the topping turn golden and the cheese starts bubbling.

If you like that irresistible bubbly crust, switch your oven to broil for the last 1-2 minutes, watching closely so it doesn’t burn. Once out, sprinkle with fresh chopped herbs like sage or basil for a fragrant finish.

How to Serve Butternut Squash Shells and Cheese Skillet Recipe

Garnishes

I like to sprinkle fresh herbs like sage or basil on top — they add a lovely brightness and fresh aroma that contrast beautifully with the rich, cheesy sauce. Sometimes a few toasted pine nuts or a drizzle of good olive oil add some extra texture and flavor if I’m feeling fancy.

Side Dishes

This skillet pairs wonderfully with a crisp green salad dressed with lemon vinaigrette to cut through the richness. Roasted Brussels sprouts or a simple steamed green vegetable like broccolini also balance the meal perfectly.

Creative Ways to Present

For a special occasion, I love serving this in individual ramekins topped with fresh herbs and a sprinkle of extra breadcrumbs. It makes it feel personal and festive, plus it’s a fun way to portion out for guests. You could even add a small dollop of mascarpone or a swirl of sage pesto on top for an elegant touch.

Make Ahead and Storage

Storing Leftovers

I store leftovers in an airtight container in the fridge for up to 3 days, and they keep surprisingly well. When reheating, I usually sprinkle a little extra milk on top and warm gently over low heat or in the oven to keep that creamy texture intact.

Freezing

I’ve frozen this recipe once or twice with decent results. Just be sure to cool it completely before transferring to a freezer-safe dish. Thaw overnight in the fridge before reheating. The texture may be slightly softer but still delicious.

Reheating

For best results, reheat leftovers gently on the stove over low heat with a splash of milk to coax the sauce back to creamy perfection. Avoid microwaving at full power to prevent the sauce from separating.

FAQs

Final Thoughts

This Butternut Squash Shells and Cheese Skillet Recipe is one of those comforting, satisfying meals that also manages to feel a bit special. I love recommending it to friends because it’s easy to make but impresses every time, with flavors that are both rich and nourishing. Whether you’re feeding family or whipping up a solo dinner, give it a try—you’ll be so glad you did!

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