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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

Cheesy Spaghetti Squash Casserole

4.85 from 32 votes
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.
prep10 mins cook1 hr 5 mins total1 hr 15 mins


  • 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
Course: Main Course, Side Dish
Cuisine: American
Keyword: casserole, healthy, spaghetti squash
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!

Megan Gilmore leaning on her white countertop.

Megan Gilmore

Hi, I’m Megan. A former fast food junkie turned best-selling cookbook author. I create healthy recipes made with simple ingredients to make your life easier.

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  1. 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!

    1. 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.

  2. 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 🙂

  3. 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.

  4. 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.

  5. 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!

  6. 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!

    1. 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!

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