Cheesy Spaghetti Squash Casserole

If you’re not sure what to do with your next spaghetti squash, try making this cheesy spaghetti squash casserole. This healthy comfort food recipe reminds me of the classic hash brown casserole my mom used to make, only this version is made with spaghetti squash, for a lower-calorie twist.

All you need is a few simple ingredients, like Greek yogurt and cheddar cheese, to get started. It also helps if you’ve already baked your spaghetti squash ahead of time, but I’ll walk you through the best ways to cook it. (I’ve tested it in the oven, slow cooker, and Instant Pot.)

Once you taste this spaghetti squash recipe, I think you’ll want to repeat it all season long! It’s naturally gluten-free and makes an easy weeknight casserole idea. Add your favorite protein to make it a complete meal!

⭐⭐⭐⭐⭐ Featured Review

“Just made this. Used sharp white cheddar and sour cream as I didn’t have yogurt. Came out fantastic! Could’ve eaten the whole pan but husband beat me to it. Will definitely make again.” – Fey

Ingredients You’ll Need

• Spaghetti Squash. Cooked spaghetti squash has a surprisingly similar texture to hash browns, and blends seamlessly into this simple casserole, while being low in calories in carbohydrates.
• Greek Yogurt. My mom’s hash brown casserole called for sour cream, so I’ve opted for whole milk Greek yogurt, which has a similar tangy flavor and a lot more protein.
• Cheddar Cheese. I use sharp cheddar cheese for a flavor boost, without needing quite as much as traditional recipes call for.
• Onion and Garlic. Sauteed yellow onion helps add another layer of aromatic flavor, especially when paired with garlic. (Though garlic powder could be used in a pinch, if needed.)

How to Cook Spaghetti Squash

The most time-consuming part of this recipe is baking the spaghetti squash, but you can do this in advance to save time. Cooked spaghetti squash can be stored in an airtight container in the fridge for up to 5 days, so I usually make this casserole when I have some stored already.

To prepare the squash, cut it in half cross-wise (through the hollow center and not the ends) and scoop out the seeds. Then follow one of the cooking methods below. Click on the links below if you’d like to see step-by-step photos.

• In the Oven: Place the squash cut-side-down on a parchment lined pan and bake for 45 to 60 minutes at 400ºF, or until the shell is easily pierced with a fork.
• In the Slow Cooker: Add a 1/2 cup of water to the pot and arrange the squash halves cut-side-down. Cover with a lid and cook on high for at least 2 hours, or on low heat for 4 to 6 hours. When the shell is easily pierced with a fork, it’s ready to use.
• In the Instant Pot: Pour 1 cup of water into the stainless steel bowl of the Instant Pot. Add the trivet that comes with your machine, then arrange the squash halves cut-side down. Secure the lid and cook at high pressure for 7 minutes. When the cooking cycle is complete, quickly release the pressure. When the floating valve in the lid drops, it’s safe to open the lid.

Once the squash is cooked, you can use a fork to pull the spaghetti-like strands away from the shell. Transfer the cooked squash to an airtight container and store it in the fridge until you’re ready to use it.

I usually get approximately 4 cups of noodles from a 3-pound squash. (If it’s a little more or less than that, it’s okay, too.)

How to Make Spaghetti Squash Casserole

Step 1:

Preheat the oven to 400ºF and lightly grease an 8-inch square pan with cooking spray. Then, heat a skillet over medium high heat on the stove top for 1 to 2 minutes. This will make the surface less likely to stick.

Add a drizzle of olive oil to the pan and cook the onion for 5 minutes, stirring often, until it starts to soften. Then add the garlic and stir for one more minute.

Transfer the cooked onion and garlic to a large mixing bowl and add the Greek yogurt, a half teaspoon of fine salt, and a quarter teaspoon of ground black pepper. Stir well.

Step 2:

Add the cooked spaghetti squash to the bowl and approximately 3/4 cup of shredded cheddar cheese. (About 3 ounces). Season with another half teaspoon of salt, then stir well to combine.

Once it looks creamy and well mixed, transfer it to the prepared pan and sprinkle the remaining cheese on top. Bake at 400ºF for 35 to 40 minutes.

Step 3:

When the cheese looks lightly golden on top, remove the pan from the oven and let it cool for at least 10 minutes before serving. You can garnish the top with freshly chopped parsley or chives, if desired.

Use a spoon or spatula to scoop this casserole for serving. It makes a comforting side dish for practically any meal you have planned.

Cheesy Spaghetti Squash Casserole

4.88 from 41 votes

If you grew up eating classic hash brown casserole, you'll love this lower calorie alternative made with spaghetti squash. It's made with creamy Greek yogurt and sharp cheddar cheese, for a comforting side dish. When you start with cooked spaghetti squash, you can get this into the oven with less than 15 minutes of prep work.

prep10 mins cook45 mins total55 mins

Servings:6

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Ingredients

 

US CustomaryMetric

 

1x2x3x

• 4 cups cooked spaghetti squash (from a 3-pound squash)
• 1 tablespoon olive oil
• 1 yellow onion , chopped
• 1 garlic clove , minced
• 1 cup plain Greek yogurt
• fine sea salt and ground black pepper
• 4 ounces sharp cheddar cheese , shredded and divided

Instructions

• Preheat the oven to 400ºF and lightly grease an 8-inch square pan with cooking spray. Heat a skillet over medium high heat for 1 to 2 minutes. (This will make the surface naturally more non-stick.) Add a drizzle of olive oil to the pan and cook the onion until it starts to soften, about 5 minutes. Then add the garlic and stir for one more minute.
• Transfer the cooked onion and garlic to a large mixing bowl and add in the yogurt. Season with ½ teaspoon of salt and a ¼ teaspoon of ground black pepper, then stir well. Fold in the cooked spaghetti squash strands and ¾ cup of shredded cheese (about 3 ounces). Season with another ½ teaspoon of salt and stir to make sure the spaghetti squash is well seasoned.
• Transfer the mixture to the prepared pan and smooth the top with a spatula. Sprinkle the remaining ¼ cup (1 ounce) of shredded cheddar over the top, then bake at 400ºF until the top is lightly golden, about 35 minutes. Your kitchen will smell fragrant as it gets close to being done, so check on the casserole when it starts to smell good.
• Remove the casserole from the oven and let it cool for at least 10 minutes before serving. You can garnish with fresh parsley or chopped chives, if desired. Leftovers can be stored in an airtight container in the fridge for up to 5 days.

Notes

Nutrition information is for 1 of 6 servings (approximately 1 cup). This information is automatically calculated using ingredients from a generic online database, so it’s just an estimate and not a guarantee. 

Spaghetti Squash Note: This recipe assumes that you’re working with the strands from a cooked 3-pound spaghetti squash. I weigh the squash using a food scale (affiliate link) to make sure it’s at least 3 pounds, but I don’t usually measure the cups that I get from the squash. So, as long as you’re using approximately that weight, it doesn’t matter how many cups you get from the squash. It should work for this recipe! 

Update Note: This recipe was originally posted in 2013 and was updated in 2025. I originally used goat yogurt and goat cheddar cheese, but since those are not always easy to find ingredients, I updated it with Greek yogurt and sharp cheddar cheese. (Which tastes a little more classic, too.) 

See the FAQ section for additional tips. 

Nutrition

Calories: 141kcal | Carbohydrates: 7g | Protein: 8g | Fat: 9g | Saturated Fat: 4g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 3g | Trans Fat: 0.002g | Cholesterol: 21mg | Sodium: 532mg | Potassium: 142mg | Fiber: 1g | Sugar: 3g | Vitamin A: 248IU | Vitamin C: 3mg | Calcium: 187mg | Iron: 0.3mg

Author: Megan Gilmore

Course: Side Dish

Cuisine: American

Keyword: spaghetti squash casserole

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If you try this recipe, please leave a comment and star rating below to let me know how you like it.