Butternut Squash, Mushroom and Fontina Pasta Bake

​​Make this warm and cozy Butternut Squash, Mushroom and Fontina Pasta Bake for a weeknight dinner or a lovely weekend meal with friends. It has roasted butternut squash, sauteed mushrooms, all mixed with cooked pasta and a cheesy white sauce, and baked in the oven with a crispy cheesy and bready topping. Serve with baguette and a good pinot.

Date Posted: 10/31/2025 | Amisha Gurbani

Gourmet mac and cheese!

My kids love mac and cheese – I mean which kid does not! But wait, they do not want just the normal boxed cheese, they love a gourmet mac and cheese, with the white sauce also called roux, made with butter and flour.

Add the macaroni and cheeses, and then bake it in little ceramic dishes with more cheese and breadcrumbs on the top, drizzled with olive oil and baked off to create a wonderful crust on the top that is so delicious!

Butternut Squash, Mushroom and Fontina Pasta Bake

Comfort food for the season – Butternut Squash, Mushroom and Fontina Pasta Bake

With fall in full swing, cold mornings sweeping in, we NEED this slightly elevated version of mac and cheese called the Roasted Butternut Squash, Mushroom, and Fontina Cheese Pasta Bake. This dish has roasted butternut squash in it, which is probably one of my favorite squashes in the family of squash, and I make it in several different ways. 

Funny thing is, I used to make SO MUCH butternut squash puree for my then babies when they were less than 1, and I would add spices to it to make it more flavorful and they loved it.

The pasta also has sautéed mushrooms. I LOVE the texture and taste of the sautéed wild mushrooms. Mushrooms are sauteed in olive oil and butter.  Add thyme, salt and pepper.

Butternut Squash, Mushroom and Fontina Pasta Bake

Mushrooms are full of flavor and add great texture and flavor to the pasta as well. Lastly I add sage leaves, fontina cheese and Parmesan cheese, which gives it all kinds of herby and cheesy flavors.  This is a very flavorful and hearty pasta bake, perfect for an anytime meal.

Ingredients for the Butternut Squash, Mushroom and Fontina Pasta Bake

The ingredients for the Butternut Squash, Mushroom and Fontina Pasta Bake are:

Roasted Butternut Squash

  • Butternut Squash
  • Olive oil
  • Salt and pepper
  • Dried thyme

Sauteed Mushrooms

  • Speciality mushrooms like Chanterelle, Oyster, Shitake
  • Salt and pepper
  • Dried thyme
  • Fats : like olive oil and butter

White Sauce

  • Fats : like olive oil and butter
  • Alliums : like onions and garlic
  • All purpose flour
  • Whole milk
  • Cheeses like fontina and Parmesan
  • Salt and pepper
  • Nutmeg
  • Lemon zest
  • Sage leaves
  • Dried pasta: I like rigatoni or shell pasta because it can hold the sauce in it

Toppings

  • Cheeses like fontina and Parmesan
  • Bread crumbs
  • Olive oil

How to make the Butternut Squash, Mushroom and Fontina Pasta Bake

Step 1

  • Roast the Butternut squash
    • This pasta is really easy. Make the dish in 4 steps. The first step is to roast the squash. Mix the cut butternut squash and spices into a baking pan, and roast at a high temperature of 425 degrees until caramelized and roasted.
  • TIP: How to cut a butternut squash?
    • Cut the butternut squash by peeling the skin off. Then cut it into half horizontally. The top half, cut it vertically into half. Then take each half, cut it into vertical slices about ¾ inch thick. Cut each vertical slice into ½ inch cubes. Repeat for the second top half side of the squash. 
    • Repeat the same process for the bottom half of the squash. Except remove the seeds and stringy pulp from the inside of each half of the squash using a spoon.

Step 2

  • Saute mushrooms
    • I love using the exotic variety of mushrooms. They are pretty to look at, and taste much better than the normal white mushrooms. The unique varieties are available at the grocery stores. Or you can find them at your local farmers market, or Whole Foods.
    • Sauteeing the mushrooms removes the water content, and cooking them in a fat like olive oil and butter makes them tasty, and also gives them a slight bite that tastes fantastic in the pasta.

Step 3

  • Make the white sauce
    • The white sauce is made with roux, which is essentially butter and flour cooked together to form a roux, until you cannot taste the flour. Smell the nuttiness of the flour cooking in the butter. Then add the milk, cheeses, spices and sage leaves for that beautiful smooth texture of a white sauce.

Step 4

  • Assembly
    • Assemble the pasta in a cast iron skillet or a baking pan, or even a lasagna pan.
    • Top with a mixture of more cheese and bread crumbs, drizzle with olive oil and bake it to perfection.
Butternut Squash, Mushroom and Fontina Pasta Bake

Tips and tricks for a good pasta bake

  • Cook the butter and flour for the white sauce for a few minutes on medium heat. You want to cut through the raw flour flavor.
  • Use a whisk for the white sauce to make a smooth mixture and whisk vigorously.
  • The topping is essential, and gives that good crunchy texture to the pasta bake. Trust me on this! 
  • For the bread crumbs – get the readymade bread crumbs from the grocery store or online at Amazon linked here
  • Make this dish gluten free, by using gluten free flour and gluten free bread crumbs that are readily available at grocery stores.
  • This is a pretty forgiving dish in the sense, add more cheese, or milk or a bit extra black pepper and it will still taste awesome! Ok do not add more salt 🙂 

We fight over the crunchy topping which is fontina and parmesan cheese, bread crumbs and olive oil, and crispy sage garnish. It is a great make ahead dish, that can be enjoyed during the week, as well as, as leftovers.

Can I make this dish ahead and bake it later?

Yes, the Butternut Squash, Mushroom and Fontina Pasta Bake can be assembled ahead of time (minus the topping) covered in aluminum foil and kept in the fridge for a day, prior to baking it. Before baking the dish, add about ½ cup milk and mix, add the topping and then bake it per the instructions.

What kind of skillet can I use to make the Butternut Squash, Mushroom and Fontina Pasta Bake?

Use a cast iron skillet or a dutch oven to make the pasta bake. Here is the link of the one that I have used to make this dish. 

How do I store the leftovers?

Leftovers can be stored in an airtight container. To re-warm it, add a bit of milk, mix and then microwave for about 1.5 minutes.

Butternut Squash, Mushroom and Fontina Pasta Bake

Other fall dinner dishes that are comforting and cozy:

If you make this dish, please do tag #thejamlab on Instagram and/or leave a comment here on this blog post!

XO
Amisha

Note: First made this recipe for the Cookfeed Magazine in 2018. Recipe revamped.

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Butternut Squash, Mushroom and Fontina Pasta Bake

Butternut Squash, Mushroom and Fontina Pasta Bake

Make this warm and cozy Butternut Squash, Mushroom and Fontina Pasta Bake for a weeknight dinner or a lovely weekend meal with friends. It has roasted butternut squash, sauteed mushrooms, all mixed with cooked pasta and a cheesy white sauce, and baked in the oven with a crispy cheesy and bready topping. Serve with baguette and a good pinot.

 

Serves 6

Scale

Ingredients

Roasted Butternut Squash

  • 3 cups (400gms) 1/2 inch cut butternut squash pieces
  • 1 tablespoon olive oil
  • 1 teaspoon table salt
  • 1/2 teaspoon black pepper
  • 1 1/2 teaspoons dried thyme

Sautéed Mushrooms

  • 2 1/2 cups(175gms) coarsely chopped exotic mushrooms like Chanterelle, Oyster, Shitake etc.
  • 1 teaspoon kosher salt
  • 1/2 teaspoon black pepper
  • 1 teaspoon dried thyme
  • 1 tablespoon unsalted butter
  • 1 tablespoon olive oil

White Sauce

  • 2 tablespoons butter
  • 2 tablespoons olive oil
  • 1 1/2 cups(200gms) finely diced white onion
  • 3 garlic cloves, finely grated
  • 3 tablespoons all purpose flour
  • 3 cups whole milk
  • 1 cup (90gms) freshly grated Fontina cheese
  • 1/2 cup (60gms) Parmesan cheese
  • 1 tablespoon lemon zest
  • 1 1/22 teaspoon table salt
  • 1 1/22 teaspoon black pepper
  • 3/4 teaspoon freshly grated nutmeg
  • 10 sage leaves finely chopped
  • 8 ounces of dried pasta(rigatoni/shell/orecchiette)

Topping

  • 3/4 cup (67gms) Fontina cheese
  • 1/2 cup (60gms) Parmesan cheese
  • 3/4 cup bread crumbs

Garnish

  • 10 sage leaves
  • 5 tablespoons olive oil
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Method

Roasted butternut squash

  • 1. Preheat the oven to 425 degrees. On a small baking pan, add the butternut squash, olive oil, salt, pepper and dried thyme. Mix it all together and lay it flat, such that it does not overlap each other. Roast in the oven for 25 minutes.

Sautéed mushrooms

  • 1. Meanwhile, prepare the mushrooms. For the mushrooms, in a medium saucepan, on medium-high heat, add the butter and olive oil. 
  • 2. Once melted, add the mushrooms, salt, pepper, dried thyme and sauté it in the pan occasionally with a wooden spatula for about 7-8 minutes till it is slightly charred. Switch off the heat. Set it aside.

Cooked Pasta

  • 1. Cook the pasta according to the packaged directions. Do not let it cook for the complete time on the package. If it says cook for 14 minutes, simply cook for 12 minutes. If it says cook for 12 minutes, simply cook for 10 minutes. The pasta will cook in the sauce, in the oven.

White Sauce

  • 1. In a large saucepan, on medium-high heat, add the butter and olive oil. 
  • 2. Once melted, add the onions and sauté for about 7-8 minutes till slightly golden brown. Add the grated garlic and sauté for 30 seconds. 
  • 3. Add the salt, pepper and nutmeg and sauté. 
  • 4. Add the flour and sauté for about 2 minutes to remove the raw taste of the flour. 
  • 5. Now add the milk. Use a whisk at this point, to whisk in the mixture well. Let it thicken for about 5 minutes. Add in the lemon zest to brighten up the flavor. 
  • 6. Add fontina and Parmesan cheeses, and whisk for 2 minutes till it reaches a smooth consistency. 
  • 7. Now add the sage leaves and mix. Switch off the heat.

Toppings and Garnish

  • 1. Mix the fontina cheese, Parmesan cheese, and bread crumbs all together in a small bowl. Keep it aside.
  • 2. In a small saucepan, add 2 tablespoons of olive oil at medium-high heat. Add the sage leaves and fry for about a minute. 

Assembly

  • 1. Preheat the oven at 350 degrees.
  • 2. Add the cooked pasta, roasted butternut squash and sautéed mushrooms in the white sauce pan. Gently mix it all together.
  • 2. Pour slowly in a 9×13 baking pan, or a 10 inch cast iron pan. Smoothen the top part. Add the topping evenly over the pasta. Drizzle the remaining 3 tablespoons of the olive oil on the top to drench the topping.
  • 3. Bake for 35 minutes on the bottom rack, and broil for about 3 minutes on high. Watch every 30 seconds to make sure that the top is not burnt. Switch off the oven. 
  • 4. Remove the baking pan or cast-iron pan gently. Let cool slightly for 10 minutes.
  • 5. Garnish with the fried sage leaves.
  • 6. Serve with crusty bread and red pepper flakes.

Notes

Can I make this dish ahead and bake it later?

  • Yes, the Butternut Squash, Mushroom and Fontina Pasta Bake can be assembled ahead of time (minus the topping) covered in aluminum foil and kept in the fridge for a day, prior to baking it. Before baking the dish, add about ½ cup milk and mix, add the topping and then bake it per the instructions.

What kind of skillet can I use to make the Butternut Squash, Mushroom and Fontina Pasta Bake?

  • Use a cast iron skillet or a dutch oven to make the pasta bake. Here is the link of the one that I have used to make this dish. 

How do I store the leftovers?

  • Leftovers can be stored in an airtight container. To re-warm it, add a bit of milk, mix and then microwave for about 1.5 minutes.

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