Cheesy Spaghetti Squash Casserole

This Spaghetti Squash Casserole tastes remarkably similar to the “Cheesy Hash Brown Casserole” that my mom used to make. Instead of using frozen hash browns, this healthy casserole features nutrient-rich spaghetti squash!

spaghetti squash casserole

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. Spaghetti squash also contains vitamins A and C, along with B vitamins, like niacin and thiamin, which are thought to help promote healthy cellular function.

My mom’s hash brown casserole called for sour cream and tons of cheese, so I’ve lightened up this version by using plain goat’s milk yogurt, which has a similar tangy flavor and creaminess.

spaghetti squash casserole recipe

Research has shown that goat’s milk is easier to digest than cow’s milk, which is why I choose to use it in any recipe that calls for dairy, but you’re welcome to use traditional dairy products if they are easier for you.

The most time-consuming part of this recipe is baking the spaghetti squash. You can speed the process by cooking your spaghetti squash in the Instant Pot, either by cutting it in half and scooping out the seeds before cooking it OR you can simply cook it whole. There are pros and cons to both methods. (Here’s how to cook spaghetti squash in the oven.)

spaghetti squash in the instant pot

I think it’s easier to scoop out the seeds from the raw squash without loosing any of the good spaghetti-strands, but the raw squash is challenging to cut.

If you cook it whole, it’s very easy to cut in half later, but then the seeds are a little more tricky to scoop out without losing the nicely cooked spaghetti squash, too.

spaghetti squash recipe

4.8 from 25 votes
spaghetti squash casserole
Cheesy Spaghetti Squash Casserole
Prep Time
10 mins
Cook Time
1 hr 5 mins
Total Time
1 hr 15 mins

ANIMAL PROTEIN  |  Gluten-free, Egg-free, Nut-free, Soy-free

Cooked spaghetti squash has a surprisingly similar texture to hash browns, and blends seamlessly into this simple hash-brown-like casserole. Combined with sauteed onions, creamy yogurt, and a bit of raw goat cheddar, this creamy dish is classic comfort food, without leaving you uncomfortable later.

Course: Main Course, Side Dish
Cuisine: American
Keyword: casserole, healthy, spaghetti squash
Servings: 8
Calories: 114 kcal
Author: Megan Gilmore
  • 1 medium spaghetti squash
  • 1 tablespoon butter
  • 1/2 yellow onion , chopped
  • 1 garlic clove , minced
  • 1 cup plain goat's milk yogurt , or greek yogurt
  • 3 oz . raw goat cheddar , shredded and divided
  • 1 teaspoon sea salt , or to taste
  • black pepper , to taste
  1. Preheat the oven to 400F and line a baking sheet with a Silpat or parchment paper. Cut the spaghetti squash in half, and remove the seeds. Place the squash halves cut-side-down on the baking sheet, and cook for 35-45 minutes, or until a fork can easily pierce the outer shell.
  2. Once you have removed the cooked squash from the oven, melt the butter in a skillet over medium-high heat and saute the chopped onion and garlic until tender and slightly golden, about 5 minutes.
  3. Transfer the cooked onion and garlic to a large mixing bowl, and combine with the yogurt and 2 oz. of shredded goat cheddar, and season with salt and pepper. When the spaghetti squash is cool enough to handle, use a fork to scrape the noodle-like strands into the bowl, and mix well.
  4. Transfer the mixture to a 2.5-quart casserole dish, and smooth the top with a spatula. Sprinkle the remaining ounce of goat cheddar over the top, and return to the oven to bake for 30 minutes at 400F.
  5. The casserole is ready when the top is a light golden brown, which makes for a crunchy crust! Serve immediately.

Per serving: Calories: 114, Carbohydrates: 10, Protein: 4, Fat: 6

healthy spaghetti squash casserole with yogurt

Recipe Notes:

  • If you’d prefer not to use goat dairy products, I think Greek yogurt and sharp cheddar cheese would be the closest substitute.
  • Vegans can feel free to try vegan cheese and yogurt as a substitute, too– just make sure the yogurt has no added sugar, or the taste will be off.
  • For those following food combining, spaghetti squash is unique in the sense that it is very hydrating and not starchy, so it can be considered “neutral” for food combining, like a vegetable. That means you can enjoy it with a high-quality meat added in to make it more of a meal-like casserole if you’d like to.

As always, if you make a modification to this recipe please leave a comment below letting us know what worked for you, so we can all benefit from your experience.

Reader Feedback: Are you a fan of hash brown casseroles? It was one of my favorite dishes growing up, so I’m happily enjoying this properly combined version now!

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denise dowst

I am going to be making this for Thanksgiving and want to know if it would work out to make it ahead of time and freeze it then bake it the day of? Would the consisting be ok or would it be weird? Thanks


    this is late but I have frozzen it when I have made it. I halfed the amount b4 baking it. then froze it and baked it a month later. it was just a yumm-o

Aileen Sabira

This looks DELICIOUS! Any ideas on what products would make it great if one was also trying to be dairy free? THANKS!

    Megan Gilmore

    I haven’t tried a dairy-free yogurt myself, but several reviewers have mentioned using plain dairy-free yogurt with success. I’d look for a brand with no added sugar, to make sure it’s tart like sour cream.


So, sorry for the silly question but what is a spaghetti squash? Thanks 🙂


    It’s a squash that has strings of the squash inside that resemble spaghetti. So if you are grain free, you can still feel like you aren’t missing out.


In typical fashion I misread and made with goat cheese..not goat cheddar. Obviously was unable to grate which is when I realized my error. It’s almost done cooking. I’m sure it’ll be yummy. Looking forward to trying again with correct cheese


I just made this for the first time last night. I used greek yogurt, regular goat cheese crumbles and I added some Italian deer sausage. OMG IT WAS AMAZING! I can see this becoming a staple for me. I’ll probably make it with some chicken sausage and freeze it for breakfasts. You could change it up so many ways! I’ve tried a lot of your recipes, love them all and this was still probably the best! Thank you!


I used natural cheddar cheese instead of goat cheese. OMG this recipe is soooo good!!


What would be considered a medium sized spaghetti squash? Or how many cups of cooked spaghetti squash is needed for this recipe? I have some leftover after making the quiche, just wondering if I have enough to make this too.

    Megan Gilmore

    Usually my spaghetti squash are about 3 pounds– probably 2 heaping cups worth?


      Perfect, I have just enough left. Thank you! By the way, that crustless quiche was awesome, even my youngest daughter ate it!


I added a bit of brown sugar to mask the tang of the Greek yogurt, which hubby doesn’t care for. He loved it. Also, I put it under the broiler fo a few minutes at the end to get the top extra brown and crunchy. Delish!!


I used your recipe as a springboard. I doubled it, and used regular shredded cheddar instead of goat cheddar, plus added frozen peas and two cans of tuna (drained). I also pulsed some Caesar croutons in my food processor and sprinkled the crumbs on top at the end, then popped it under the broiler until they browned.


I had leftover spaghetti squash and was looking for a recipe to use it. This was perfect since I already had the squash baked. However I did not have plain Greek yogurt on hand so I used sour cream in a pinch and it worked great! The whole family loved it, I would definitely make this again and again! Thank you!

Lyn :]

Well I went to make this recipe and low and behold had no cheddar cheese , so I substituted with pecorino romano. Oh my Word this was soooooo delicious!!! I wish I could give it a ten rating!!! So indebted to you for my great dinners, :] Lyn :]


Really delicious! Even my kids who proclaim that they “hate squash” ate it!


This is one of my favorite spaghetti squash recipes. I made it as a side dish with asparagus and blackened shrimp and it was a hit! My boyfriend went back for seconds just for the spaghetti squash! I used greek yogurt. I didn’t see a goat cheese that said cheddar, so I bought the goat cheese that was in block form to shred. Must try!


This was a super yummy side dish! I did use full fat sour cream and regular cheddar cheese (I’m on a low carb diet recommended from my endocrinologist to try to control my diabetes & drop weight) & this has to be one of the best side dishes I’ve had- it really feels like hash Brown casserole and tastes amazing. Thank you!


I made this for dinner tonight. It was very good! I used the pressure cooker to cook the squash and it came together easily. Cheesy spaghetti squash was a satisfying substitute for cheesy potatoes. Thank you!

Emily L Patrick

I made this, amazing, no leftovers!


I have this in the oven now. I added shredded chicken breast and ricotta cheese and used sharp cheddar. It smells good. Thank you for your recipe

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