This Spaghetti Squash Mac and Cheese is loaded with cheesy flavor and it’s a great way to satisfy your macaroni and cheese craving without pasta!

Spaghetti Squash Mac and Cheese
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I love spaghetti squash and I love macaroni and cheese so spaghetti squash macaroni and cheese seemed like a natural thing to try! A simple cheese sauce comes together quickly and this is an easy way to add more veggies to your plate. I also think this would be a kid-friendly way to introduce them to this winter squash!

How to Make Spaghetti Squash

There are a few ways to cook the spaghetti squash for this recipe. I recommend the microwave because it’s the fastest option, but you can also cook it in the oven.

Microwave method: Carefully slice your spaghetti squash in half. Scoop out the seeds and flip the halves cut side down on a large microwave-safe plate. Add a little water to the bottom of the plate (to create steam) and microwave on high for 10 minutes. Remove from the microwave, let cool slightly, then use a fork to scrape out the strands. For this recipe, you don’t want to overcook the squash since you’ll be putting it in the oven.

Oven method: Carefully slice your spaghetti squash in half. Scoop out the seeds and flip the halves cut side down on a large baking sheet. Bake at 400 degrees for 20-25 minutes until softened. Let cool slightly, then use a fork to scrape out the strands. For this recipe, you don’t want to overcook the squash since you’ll be putting it back in the oven. I recommend only baking for 20 minutes, then scraping out the strands.

Instant Pot method: You can actually cook spaghetti squash in an Instant Pot which is quick and easy! Check out the blog post for the full instructions.

spaghetti squash macaroni and cheese on a fork

Tips & Substitution Ideas

  • I used dairy milk for the cheese sauce but I’ve also made it with almond milk. Almond milk is a little less creamy, but it works.
  • I highly recommend using a block of cheese and shredding it by hand rather than buying pre-shredded cheese. Pre-shredded cheese has anti-caking agents in it and it tends to clump rather than melt.

How to Make Spaghetti Squash Mac and Cheese

Cook the spaghetti squash until tender. Scoop the strands out with a fork. Heat the cheese sauce on the stovetop then combine the sauce with the spaghetti squash. Top with a little extra shredded cheese, if you like! Bake until cheese is melted.

Greek Yogurt Cheese Sauce

In an earlier version of this recipe, I included a cheese sauce made with almond milk and Greek yogurt. For that version, you’ll need 1 cup of almond milk, 2 tablespoons of flour, 1/4 cup of plain Greek yogurt, and 1 cup of shredded cheddar cheese. Follow the directions below, using the amounts listed above and stirring in the Greek yogurt with the shredded cheese. This sauce is a little less rich but it’s a lower calorie option.

More Spaghetti Squash Recipes

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Spaghetti Squash Mac and Cheese

Spaghetti Squash Mac n Cheese

5 Stars 4 Stars 3 Stars 2 Stars 1 Star 5 from 5 reviews
  • Author: Liz Thomson
  • Prep Time: 15 mins
  • Cook Time: 15 mins
  • Total Time: 30 mins
  • Yield: 6 1x
  • Category: Vegetarian
  • Method: Oven
  • Cuisine: American
  • Diet: Vegetarian

Description

This cheesy spaghetti squash is a delicious and simple dinner recipe that is packed with vegetables! If you love macaroni and cheese but you want a healthier option, this is a great alternative!


Ingredients

Units Scale
  • 1 medium spaghetti squash (About 5 cups of shredded squash)
  • 2 tablespoons butter
  • 1 cup milk (2%, skim, or whole milk)
  • 1 cup shredded cheddar cheese
  • 2 tablespoons flour
  • 1/2 teaspoon salt
  • Additional salt & pepper to taste

Instructions

  1. Preheat oven to 400 degrees.
  2. Slice the spaghetti squash in half and discard the seeds.
  3. Turn it upside down (so the peel is facing up and the inside is facing down) and place it on a large plate. Add a bit of water to the plate and cover with a paper towel.
  4. Microwave for 10-15 minutes, or until the inside is soft. Once it slightly softened, scoop out the strands with a fork.
  5. In a large saucepan, melt the butter over medium heat.
  6. Whisk in the butter and continue to cook for 30 seconds.
  7. Reduce heat to low and add milk. Whisk until smooth.
  8. Remove from heat and stir in shredded cheese. Whisk until melted.
  9. Combine the spaghetti squash with the cheese sauce and place in a casserole dish.
  10. Bake for 15-20 minutes until the cheese is bubbly.
  11. Remove from oven and sprinkle with salt and pepper.