Cheesy Spaghetti Squash Casserole

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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
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4.84 from 30 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!

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Danielle @ Clean Food Creative Fitness

This looks great! I would never think to use the Greek yogurt to give it some extra creaminess but I bet it’s delicious!


I have been enjoying your site and all the wonderful recipes for quite some time now. I just so happen to have a fresh spaghetti squash that is begging to be made into this! lol.

Ana @

I love it! I will definitely be making this asap!!

tayler alexis


im going to whole foods now to get spaghetti squash ! i have got to try this tonight !!


OMG this looks so decadently delicious!! I have never tried goat cheddar. Any brands that you recommend for a first-timer?


    Alta Dena’s goat cheddar is a little more mild, and is the first brand I ever tried and enjoyed. I tend to like stronger, more “stinky” cheeses, so now my new favorite is Mt. Sterling’s extra-sharp raw goat cheddar. I believe they have a mild version, too! Both brands are very tasty. 🙂


      Thanks Megan! Crossing my fingers that Wegmans carries it!


This looks insanely good! I will be trying this as soon as I get my hands on all of the ingredients. 🙂


That is like, perfect winter food!


This was good! Thanks! 🙂


Can you eliminate the cheese? Thanks!
And can you use summer squash “noodleized?”


    Eliminating the cheese will greatly change the flavor, and you’ll miss the crispy crust on top. Also, using summer squash will change the texture and flavor. Probably won’t taste like a hash brown casserole anymore, but I’m sure you could have fun experimenting!


This sounds absoultely amazing and I am going to make this. I love all of the squash family and I always have so much from the garden and it seems mostly spaghetti squash so this recipe will come in handy. Thank you so much and I love love love many of your recipe ideas.


I would love to try this but my family is vegetarian and some vegan. What can I use instead of goat cheeze and greek yogurt?


    Perhaps there are vegan versions of plain yogurt or cheese you could try. Since I haven’t made it myself, I couldn’t tell you exactly!


Hi Kai-I am vegan and I used plain soy yogurt and Daiya mozzarella cheese, and it is so delicious!

Linda Wagner

O.M.G. I literally ran to the store to get the greek yogurt so I could make this. Spaghetti squash is in the oven!!! I’ve said it before and I’ll say it again, you are a genius!! xo


Hi Megan. I made this tonite and loved it. I am wondering if you have any ideas to add a little crunch to (the top) of it? So nice to have some tasty healthy food during these cold winter months!


    I would use TVP 🙂


I just made something similar using shredded cabbage that had been blanched instead of squash. It was great and a great way to eat cabbage if you are not a huge fan. Cheese makes everything wonderful!


This looks fabulous, thx for sharing!


I just assembled this now for dinner in a few hours! It look amazing! So far all of your recipes have been delicious! I love these kinds of “clean” recipes. I used regular goat cheese like a Chèvre since I didn’t have any goat cheddar, so hopefully it will be just as good. I love the creaminess of it! Enjoy your site blog and my weekly emails for you Megan!

Alyssa S.

I made this last night for a girls night dinner/bachelor marathon and it was SO GOOD. I seriously cannot wait to eat the leftovers tonight!! Thanks for the recipe, it will be a new staple!


Megan! I made this last Night for dinner and ohh my was it ever good! Im have the leftover for lunch today! This dish is perfect for the stormy weather we have in canada


Thank you so much for you yummy experiments. This is very good. I would have to agree that cheese makes lots of things taste better.


Prepared this last night, it was fabulous! Next time I am going to try it with scallions. Thanks for ANOTHER great recipe.

Andria Miller

This does look great, but isn’t it improperly combined? spaghetti squash is a starch which is paired with dairy. I’m sorry if you addressed already, I read through the post/comments quickly.

Also, my other question, as I am new to reading your blog (love it BTW!) are you still following a grain free program? I aw a rice dish on your most rece t “what I ate.” Thx!


    Due to its high water content, spaghetti squash actually is considered neutral for food combining purposes. So this dish is properly combined!

    In regards to a grain-free lifestyle, my husband and I only experimented with a “strict” program for 30 days in January last year. Since then, we’ve included grains in our meals whenever we feel the desire for them. In general, I prefer not following any strict dietary guidelines or programs, because I think that would drive me crazy in the long run!

Andria Miller

Great! I am happy to hear your response because I really do enjoy cheese on my spaghetti squash! I feel I have been trying to set too many strict dietary guidelines for myself which DOES drive me crazy (speaking of a 30 day paleo challenge I tried to do a Whole30 which is super strict and didn’t get past 16 days) and I am wondering if the more restrictive I am the more issues(ie digestive) I have because I lose tolerance for stuff (???)

I really do enjoy your blog and your recipes look great! And, like you, I have a sweet tooth, so I’m super excited to work my way through your desserts!

Brittany Martinez

Anyone tried coconut milk yogurt for this?


Made this last night for a dinner party – DELICIOUS! I followed the recipe to the letter and people kept saying how much they loved the spaghetti squash.

Erika G.

I made it tonight and it was soooo yummy! Instead of the yogurt, I used an avocado (blended with some water until the consistency of yogurt). The avocado makes it not combined with the cheese, but its easier for my tummy than the yogurt AND cheese. Also, I roasted a bag of frozen organic broccoli on the pan while cooking the spaghetti squash and added it in before baking. Extra flavor and texture. It turned out a little green, but if you don’t mind (or want a St. Patrick’s day recipe)…it’s a winner.


Mmm, just finished a helping and it was delicious! Rich, but delicious! My husband and kids gobbled it up too. So happy to have stumbled upon your site 🙂


Where are some of your stops for buying goat cheese? 🙂 This looks fantastic!


    I usually have the best luck at Whole Foods.


I’ve made this twice in two weeks for my family. I can’t believe how much my kids love it! Mine has been on the watery side when it’s done. I followed the recipe to a T, should it be a little runny when it’s done? Still tastes good, but yours sure does look firmer than mine!


    I’d assume the watery texture is coming from the spaghetti squash– some are more moist than others! I’d make sure you’re baking it long enough (before making this casserole), to ensure that as much moisture is removed as possible.


delicious! I added some roasted quinoa to the top for a little bit of a crunch!


This was wonderful!!! I added a red pepper in with the onion and the garlic. It added a nice crunch! Is there a trick to “shredding” goat cheese? I love your site! You make eating healthy so delicious!!!


Made this tonight….flippin’ AWESOME!! I could eat the entire dish, had to make myself stop!!! Love your site and all the recipe ideas…ROCK ON!!


I tried a lot of your recipes and have been completely enjoying eating cleaner. I absolutely LOVE cooking and all these new recipes are extraordinary! Thank you for sharing it all… this dish is one of my absoooolllluteeee favoritessss!! It’s great with any course- bfast, lunch or dinner… Amazing.


You can make the squash the same way and add your fav speghetti sauce. Very yummy as well. :o)


I don’t understand how this dish fits the Food Combining Chart, since squash is a starch and cheese/yoghurt obviously a protein 🙁


    Spaghetti squash is unique in the fact that it has a very low starch content, making it “neutral” for food combining purposes. You can consider summer squash, like yellow and zucchini, neutral as well. Winter squash, like butternut and acorn, are the type that must be considered starches.


      Wow, thanks for this explanation! Where I grew up, we’ve never really had so many different types of squash. On second thought, we actually might have had them all, but apparently I never paid enough attention. In any case, thank you so much for the great recipe and the additional info 🙂


Bought chevre because it wasn’t really specified as to what kind of goat cheese. Going to make it anyway and see how it goes.


    Made it with the soft goat cheese and it was a hit!


I made this today with nonfat yogurt and daiya cheddar cheese (we avoid animal fats, hence the dairy nonfat yogurt but no dairy cheese). I didn’t have garlic but sauteed some mushrooms in with the onions… then I mixed nutritional yeast into the yogurt/daiya sauce and sprinkled some on top with the daiya for added nutrition and flavor… came out great!!!


Can you use shredded cheddar cheese instead of goat cheese? Thanks!


    Yes, definitely.


Love this!! Just made it for our family and it turned out great. Thanks for posting!!


I just made this and it was delicious! I am on a low carb dieter following the medifast plan and this works well with a few minor changes! I just posted it on my blog! Thanks for a great recipe!


I mean it works well with the Medifast plan with a few minor changes. 🙂


Love love love this! Had it last night! I used regular shredded cheddar instead of the goat and it still turned out great!!


This way amazing!! My one year old went crazy about it!! Great substitue for Mac n’ Cheese!


My husband would love this with a layer of my bolognese sauce to the casserole. Possible?


Heyya, looks amazing but I have never come across spaghetti squash before? I have made zucchini spaghetti with a special peeler, is that the same thing?

Thanks 🙂


OMG this looks amazing! Going to have to go get some squash 🙂


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!

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