Spaghetti Squash Mac and Cheese

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This spaghetti squash mac and cheese comes complete with a homemade cheese sauce and breadcrumb topping. Bake it to perfection in under an hour!

Spaghetti squash ma and cheese with a fork.

Amazing Spaghetti Squash Mac and Cheese

Is there a better combination in the fall than savory squash and a homemade cheese sauce!? We think not!

You’re going to love this ultimate fall comfort dish that brings together the sweet and savory flavors of spaghetti squash with a homemade cheese sauce and bread crumb topping.

Spaghetti squash mac and cheese ingredients on a baking sheet.

Featured Ingredients

This spaghetti squash comes together in 3 parts — roasting the squash, preparing the breadcrumb topping and making the cheese sauce.

For the squash

  • Spaghetti squash
  • Olive oil 
  • Salt & pepper

For the bread crumb topping 

  • Corn flake crumbs 
  • Shredded mozzarella cheese
  • Garlic powder 
  • Dried thyme
  • Dried parsley 
  • Red pepper flakes
  • Salt 
  • Olive oil

For the Cheese Sauce 

  • Unsalted butter
  • All purpose flour 
  • Whole milk 
  • Shredded mozzarella cheese
  • Shredded gouda cheese
  • Chipotle hot sauce
  • Salt & pepper

mac and cheese

try it!

Butternut Squash Mac and Cheese

Looking for more squash mac and cheese recipes? You’ve got to try our butternut squash mac and cheese.

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Spaghetti squash on a baking sheet.

How to Make Spaghetti Squash Mac and Cheese

Prep spaghetti squash

Use a large, sharp knife to carefully slice the spaghetti squash in half lengthwise (hotdog style). Remove the innards of the spaghetti squash out with a spoon. 

Drizzle about 2 teaspoons of olive oil over each half of the spaghetti squash and then season with ¼ teaspoon of salt and ¼ teaspoon of ground pepper. Place the spaghetti squash open side-down on the lined baking sheet and bake for 20 minutes at 400ºF. 

After 20 minutes, flip each half of the spaghetti squash over and bake for another 20 minutes. We recommend checking the squash with a fork after 10 minutes to make sure your spaghetti squash isn’t getting mushy. Every oven is different so the time may vary. 

Prep mac and cheese topping

Add the corn flakes to a food processor and process until the corn flakes look like breadcrumbs. Add garlic powder, thyme, parsley, red pepper flakes, salt and mozzarella cheese to the food professor and pulse until just combined. Set aside for later. 

Prep mac and cheese sauce

Heat a small saucepan over medium/high heat. Add butter. When the butter is melted add the cracked pepper corns to the butter. When the pepper is fragrant, add flour and whisk until the butter and flour form a paste.

Slowly add milk to the pot, whisking constantly. Continue to whisk the roux over medium heat for about 4-6 minutes or until the roux thickens.

When the roux is thick, remove from heat and add the gouda cheese and mozzarella cheese. Stir until the cheese has melted. Add the hot sauce and salt  to the cheese sauce and mix again to combine.

All together now

Remove the spaghetti squash from the oven and let it rest for 5 minutes before carefully “fluffing” the edges of the squash with a fork to loosen the spaghetti squash from the skin of the skin. 

Turn the heat on the oven to broil. Pour half of the cheese sauce into each half of the fluffed spaghetti squash and gently toss the “spaghetti squash noodles” with the sauce until they are coated. 

Broil with topping & enjoy!

Top each spaghetti squash half with 2-3 tablespoons of the corn flake topping and drizzle the olive oil over the tops of each squash. Place the squash in the oven and broil until golden brown.

Spaghetti squash and cheese sauce on a baking sheet.

Top Tips for Spaghetti Squash Mac and Cheese

Size matters: We used a 1.75 lb squash for this recipe. The size of squash will determine how long you have to bake your squash. 

Choose your cheese: You can change up what type of cheese you use. We recommend trying sharp yellow or orange cheddar.

Let’s talk peppercorns: We crack whole peppercorns using a mortar and pestle. If you don’t have a mortar and pestle then you can use a pepper grinder.

Spaghetti squash mac and cheese topped with breadcrumbs.

Storage

To store spaghetti squash mac and cheese, let it cool completely and then place it in an airtight container before placing it in the fridge for up to 5 days.

To reheat: we recommend reheating this spaghetti squash mac and cheese covered in the oven at a low heat until warm. Add broth by the tablespoon to thin out the sauce if need be.

Spaghetti squash mac and cheese on a fork.

Spaghetti Squash Mac and Cheese

This spaghetti squash mac and cheese comes complete with a homemade cheese sauce and breadcrumb topping. Prep and serve in under an hour!

Prep:20 minutes

Cook:50 minutes

Total:1 hour 10 minutes

Fat 35

Carbs 18

Protein 22

Ingredients

  • 1 2-lb. spaghetti squash
  • 1 tablespoon olive oil separated
  • ½ teaspoon salt separated
  • ½ teaspoon ground black pepper separated

Cheese Sauce

  • 2 tablespoons unsalted butter
  • ½ teaspoon cracked peppercorns*
  • 2 tablespoons all purpose flour
  • 1 cup whole milk
  • ½ cup shredded mozzarella cheese
  • ½ cup shredded gouda cheese
  • 1 teaspoon chipotle hot sauce
  • 1 teaspoon salt

Instructions 

  • Preheat the oven to 400ºF and line a baking sheet with parchment paper.

  • Next prepare the spaghetti squash. Use a large, sharp knife to carefully slice the spaghetti squash in half lengthwise (hotdog style). Remove the innards of the spaghetti squash out with a spoon.

  • Drizzle about 2 teaspoons of olive oil over each half of the spaghetti squash and then season with ¼ teaspoon of salt and ¼ teaspoon of ground pepper.

  • Place the spaghetti squash open side-down on the lined baking sheet and bake for 20 minutes at 400ºF.

  • While the spaghetti squash is baking, prepare the mac and cheese topping. Add the corn flakes to a food processor and process until the corn flakes look like breadcrumbs. Add garlic powder, thyme, parsley, red pepper flakes, salt and mozzarella cheese to the food professor and pulse until just combined. Set aside for later.

  • After 20 minutes, flip each half of the spaghetti squash over and bake for another 20 minutes. We recommend checking the squash with a fork after 10 minutes to make sure your spaghetti squash isn’t getting mushy. Every oven is different so the time may vary.

  • While the spaghetti squash is baking, prepare the cheese sauce by making a roux. Heat a small saucepan over medium/high heat. Add butter. When the butter is melted add the cracked pepper corns to the butter. When the pepper is fragrant, add flour and whisk until the butter and flour form a paste. Cook the paste for about 1 minute.

  • Slowly add milk to the pot, whisking constantly. Continue to whisk the roux over medium heat for about 4-6 minutes or until the roux thickens.

  • When the roux is thick, remove from heat and add the gouda cheese and mozzarella cheese. Stir until the cheese has melted.

  • Add the hot sauce and salt to the cheese sauce and mix again to combine. Set cheese sauce aside.

  • Remove the spaghetti squash from the oven and let it rest for 5 minutes before carefully “fluffing” the edges of the squash with a fork to loosen the spaghetti squash from the skin of the skin.

  • Turn the heat on the oven to broil.

  • Pour half of the cheese sauce into each half of the fluffed spaghetti squash and gently toss the “spaghetti squash noodles” with the sauce until they are coated.

  • Top each spaghetti squash half with 2-3 tablespoons of the corn flake topping and drizzle the olive oil over the tops of each squash. Place the squash in the oven and broil for 1-2 minutes or until golden brown. Be sure to keep an eye on the squash as every broiler is different.

  • Remove the squash from the oven and enjoy.

Tips & Notes

  • We used a 1.75-lb squash for this recipe. The size of squash will determine how long you have to bake your squash.
  • We crack whole peppercorns using a mortar and pestle. If you don’t have a mortar and pestle then you can use a pepper grinder.
  • You can change up what type of cheese you use. We recommend trying sharp yellow or orange cheddar.

Nutrition facts

Calories: 471kcal Carbohydrates: 18g Protein: 22g Fat: 35g Fiber: 1g Sugar: 3g



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