Ready for a Summer Reset? Get your copy → tiny summer reset book cover

Cheesy Spaghetti Squash Casserole

This post may contain affiliate links. Please read my disclosure and privacy policy.

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

spaghetti squash casserole
Print Pin
4.82 from 27 votes

Cheesy Spaghetti Squash Casserole

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
Prep Time 10 minutes
Cook Time 1 hour 5 minutes
Total Time 1 hour 15 minutes
Servings 8
Calories 114kcal


  • 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


  • 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.
  • 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.
  • 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.
  • 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.
  • The casserole is ready when the top is a light golden brown, which makes for a crunchy crust! Serve immediately.



Calories: 114kcal | Carbohydrates: 10g | Protein: 4g | Fat: 6g | Saturated Fat: 3g | Cholesterol: 18mg | Sodium: 404mg | Potassium: 198mg | Fiber: 1g | Sugar: 5g | Vitamin A: 325IU | Vitamin C: 3.3mg | Calcium: 143mg | Iron: 0.5mg
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!

Shop the Post:
Get more recipes + meal plans in my books:

detox book and meal plan

Never Miss a Post!

Get a FREE 3-Day Detox Plan when you sign up for my email newsletter

Leave a Reply

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.



what else could use instead of yogurt? im trying to use what I have here without having to make a trip to the store! LOL. I was wondering 1% milk but that would make it watery?


I made this tonight and the whole family and I loved it. I used almond milk yogurt instead but followed recipe exactly otherwise. Btw it’s your recipe of almond yogurt and its fantastic.


Just made this, and it was absolutely delicious! I didn’t change a thing, followed the recipe exactly. It’s an amazing feeling to be able to eat this rich-tasting food, without the horrible indigestion after. Thanks for another keeper Megan!


Hi, Megan! I made this recipe last week and it was super delicious! It’s a healthy comfort food option.
Thank you!


I tried making this the other day. I couldnt find raw goat chedder so I picked up goat chesse crumble (never having tried any kind of goat cheese) and it was horrible lol. I’m going to check the other grocery stores around and hopefully I can find the right cheese!

sarah thompson

Ohhhhhhhhh this was good! I do have to admit that since my family doesn’t exclude dairy, I went all out and used sour cream for the yogurt and shredded cheddar for the goat cheese. I also made some bread crumbs with udis GF bread and garlic and sprinkled them on top. Probably not as clean as most of your readers are looking for, but for this wheatless family, it was PERFECT! Thank you for helping us to not only be wheat free, but able to hide some veggies too 🙂


Making this casserole for the second time this week! It is going to be served as part of a GAPS legal meal I’m preparing for our extended family during the holidays.


I used yogurt and cheddar but added. sauted chicken bites to make casserole my hubby would eat. Its still in the oven and smells gteat. Will let you know what he says.


This is my first time visiting your site, found you off pinterest and LOVE everything about this place!!! Very excited to try some of these recipes out on the Hubby…he doesn’t care what he eat, but I am trying to be very careful, so if when I can find something that is good for me and pleases him I consider it a win!

Kristy Bryan

I made this tonight…It was good, and my husband liked it a lot! I was not expecting the spaghetti squash to have a bit of a crunchy texture though. It kind of reminded me of potatoes that aren’t cooked completely. Is that normal? If I had baked the squash longer, would it have softened up more? I baked it for 40-45 minutes before making it into the casserole. This was my first experience with spaghetti squash. It was pretty cool, however, watching the “noodles” appear when I scraped out of the shell. I would appreciate your feedback. Thanks for the recipe and your website. I am new at food combining, but am already feeling that my digestive track is improving and I am losing weight. That, is great!


    Spaghetti squash does have a unique texture. It’s more hydrating and slightly crunchy, but certain squashes are “crunchier” than others. I’ve found that if I bake them long enough so that a brown spot develops on the outer skin, the texture of the “noodles” is better on the inside. Hope that helps!


I tried this tonight and was super stoked but for some reason the tang from the Greek yogurt was very prominent in mine 🙁 what did I do wrong?

Toni P

I made this tonight and I added mustard powder and cayenne to balance out the tang of the yogurt. YUMMMM


When I made this recipe which was AMAZING! I found it to be on the tad watery side. Not sure what made it so watery. It was GREAT non the less just wondering what I could do to reduce the amount of liquid that is on the bottom of the caserole. Thanks!


Oh my gosh….I’m currently trying this for the first time and it is going to take some SERIOUS will power to not eat the entire dish

Added some chili powder to combat the tanginess (thanks above reviewer!) and it is GREAT


Megan, this was a big hit in our house! Made this last week, and 19-year-old daughter has been requesting that I make it again. Needless to say, this will be a regular meal in our home – will shake it up by adding other veggies and/or cheeses. Thanks!! Next, plan on trying the veg fried rice and want to re-try the cauliflower pizza crust. Think I didn’t squeeze enough moisture out of cauliflower.


    If you have access to a juicer, “juice” your cauliflower- the non-juice pulp is doughy-like so mixed with eggs and cheese, it bakes up well because all of the water has essentially removed by the juicing process. And, you can use the juice for soups, too.

Anna D

This recipe is absolutely delicious! I’m not a fan of onions so I didn’t saute the onions, garlic and butter but rather melted the butter and just mixed it with garlic. As well I am not vegan so I just used regular marble cheese. So delicious, tastes much better than expected! And so creamy with the yogurt 🙂


Just stumbled across your site and there are so many yummy recipes that I cant wait to try. This one reminds me of the Cheesy Noodle Casserole my mom made us when we were kids…still a favorite but this might be the healthier version I have been looking for.



Made this today and it came out delicious! Couldn’t find any raw goat cheese anywhere so used the cow’s raw cheddar cheese and it was great!


Can I put normal cheddar cheese for my kids?


    Yes, definitely!


I made this and I left out the cheese because I didnt have any. I put smoked paprika on top and it tasted like scalloped potatoes!!! I am making it again right now with the cheddar! Thanks for the recipe


This sounds delicious! I have never had spagetti squash before. What might you serve this recipe with?


OMG!! I love this recipe, I can gain weight just eating it , I want to to eat it all up. I can’t even taste the squash. And it fits in my Atkins diet, I can’t believe it…. just delish!!

Jackie Mac

This recipe is so good!!!


Yet another amazing dish…LOVED


Thank you SO MUCH for adding printable versions of your delicious recipes at the end of your entries! I can’t wait to try some of them and this one (spaghetti squash ‘hash-brown’ casserole) will be FIRST!


I love your recipes so much! I have made this spagetti squash casserole before and its fab, but was wondering if you can make it with cultured coconut (unsweetened) instead of yogurt? Thanks!!!


This was delish! Hubby even loved it even after forgetting the yogurt:) Thank you for posting this recipe!!


Do you think I could use sour cream instead of the yogurt?


    Yes, that would provide a similar flavor and texture.


I made this tonight and added some mushrooms and kale in with the onions and garlic, plus a scoop of white miso paste and red pepper flakes. Came out SO good!! Thanks for the recipe!


    Omg that sounds so good


How on earth is all that cheese on top just 1oz. I am starring at 4 ounces of shredded cheese And this alone is just enough for the top, I would have to do 4 more for for the dish it self.


    I take it back, I think I envisioned using a bigger pan, it was enough. I just died and went to heaven, omg it’s sooooooo good. The cheese and yogurt together make it seem like I used ricotta even though I didnt. I just ate half the dish, I can’t stop. This is going at the top of my comfort food list. Thank you, thank you, thank you


Cheesy-Spaghetti-Squash-Casserole looks and sounds GREAT!!! I’m a very brittle diabetic and have to be strict and count all carbs. Can you tell me how to come up with the carbs according to the recipe? Thanks!


    You can use a free nutrition calculator at or to calculate any numbers you need.


Can you prepare the spaghetti squash ahead of time and then mix it up when you’re ready? Also, what sides would you serve with this? I’m new to clean eating.

Stephanie Jacobs

Just want you to know that I LOVE this recipe, I make it all the time! I’m going to be so sad when spaghetti squash goes out of season and I can’t make it until next year. Great job!!!


Hi Megan,

What kind of meat would taste best in this if I added meat? Thanks!

    Megan Gilmore

    I’ve added chicken to it before and my family loved it!


I have made this several times; it is so delicious and always a hit! Our garden is going crazy right now with yellow squash, so I was thinking of substituting them (in “spiralized” form) for the spaghetti squash. I was curious if anybody had tried this already and could offer any feedback on how it turned out?


Used shredded organic cheddar instead of goat- ended up tasting like a healthier/better version of Cracker Barrel’s hashbrown casserole! Did get some watery-ness at the bottom of the dish- thinking maybe my glassware was too small and would have required more time in the oven to fully cook through? Regardless- it was great!

Never Miss a Post!

Get a FREE 3-Day Detox Plan when you sign up for my email newsletter