This easy, and cheesy vegetarian spaghetti squash gratin is rich in protein, low-carb, and gluten-free. It’s perfect as a holiday side dish or prep ahead weekday meal. Plus, it’s topped with a secret, crunchy topping. 

What is Spaghetti Squash?

Let’s talk about spaghetti squash for a hot minute. Spaghetti squash is a lower carb squash that’s available year round but is in season in the Fall. When cooked, the inside can be scraped into stringy, spaghetti-like strands. It’s the perfect low-carb and low-calorie pasta substitute, with a good amount of fiber and B vitamins. 

How do you cook spaghetti squash?

Great question. Spaghetti squash can be a P.I.T.A. to prepare, and even dangerous, too. Be especially careful when cutting it open so you don’t cut off a finger (or hand). Here’s the OG method for cooking spaghetti squash (the method I still follow):

  • Step one: Cut spaghetti squash in half lengthwise using a large knife (be careful!). 
  • Step two: Scoop out inner seeds and stringy pulp. 
  • Step three: Spray insides with cooking oil spray (or rub a little bit of olive oil). Season with salt and pepper.
  • Step four: Place spaghetti squash halves cut-side-down onto a foil-lined baking sheet. Bake until skin is easily pierced with a fork. Here are some approximate cooking times for a medium-sized squash at different temperature. These times may vary depending on the size of your squash. 
    • 375°F for 50-60 minutes
    • 400°F for 40-50 minutes
    • 425°F for 35-45 minutes

*Note: we won’t be cooking the squash as long for this recipe because it’ll be cooked again in a baking dish once mixed with the other recipe ingredients.

  • Step five: Let cool before using a fork to scrape out the spaghetti-like strands.

If you’re not feeling this method, here are some other ways of cooking spaghetti squash:

  • In the Instant Pot: This method cuts the cooking time significantly, and you’ll end up with perfectly cooked spaghetti squash in around 15 minutes. 
  • In the Microwave: I’ll admit, I’m not a huge fan of this method because the end result is a little mushier and wetter. However, it’s much faster! 

 How to store spaghetti squash

Cooked, plain spaghetti squash strands can be stored in the fridge and used for up to a week. This cheesy spaghetti squash bake can stay good in the fridge in an airtight container for about 3 to 5 days and is best served reheated. 

Here’s What You’ll Need to Make This Spaghetti Squash Gratin

These are the main ingredients you’ll need:

  • Spaghetti Squash: Well, duh. I used a medium-sized spaghetti squash, about 2 – 3 pounds.
  • Eggs: Eggs are used in this recipe as a binder, to hold the spaghetti squash strands together. They also contribute protein to this dish. 
  • Cheese: I use white cheddar cheese for this dish, but feel free to use another type of cheese like regular cheddar or even mozzarella. If dairy-free, see substitution options below. 
  • Greek yogurt: Greek yogurt adds a little creaminess and an extra boost of protein to this dish. If dairy-free, see substitution options below. 
  • Fresh thyme: I love adding a little fresh thyme to this dish. If thyme isn’t your thing, you can use other fresh herbs like rosemary or basil. 
  • Watusee Foods Chickpea Crumbs: My secret ingredient! These breadcrumb-like chickpea crumbs make for the perfect crunchy topping for this spaghetti squash gratin. They’re made from just one, yes one, ingredient: organic chickpeas. They’ve got the flavor and crunch that I love in regular breadcrumbs but with more fiber and protein. Plus, they’re gluten-free so they can satisfy the dietary needs of friends and family. 

Recipe Substitutions

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  • Dairy-free: To make this dairy-free, you can sub out the Greek yogurt for a plain, unsweetened dairy-free yogurt and use a dairy-free shredded cheese alternative, like this Plant-Based Cheddar Cheese from Whole Foods. If you avoid butter as well, you can use a dairy-free butter like Earth Balance or Miyoko. 
  • Keto-friendly: Spaghetti squash is a keto favorite because it’s low in net carbohydrates, at just 8 grams net carbs per cup. Plus, the remaining ingredients for this dish, like eggs and cheese, are also pretty low in carbs. You may want to reduce or eliminate the chickpea breadcrumbs to make this truly keto, since it will contribute carbs. 

Let’s get cooking! If you make this recipe I’d love to see it! Feel free to share on Instagram and tag me @shapedbycharlotte so I can see it.

Gluten-Free Spaghetti Squash Gratin

Gluten-Free Spaghetti Squash Gratin

Yield: 6 - 8 servings
Prep Time: 15 minutes
Cook Time: 1 hour
Total Time: 1 hour 15 minutes

This easy, and cheesy vegetarian spaghetti squash gratin is rich in protein, low-carb, and gluten-free. It's perfect as a healthy holiday side dish or prep ahead weekday meal. Plus, it's topped with a secret, crunchy topping. 


  • 1 medium-sized spaghetti squash (about 2.5 pounds)
  • 2 large eggs
  • 1/2 cup plain, whole milk (or 2%) Greek yogurt
  • 1 cup shredded white cheddar cheese
  • 1/2 small yellow onion, finely chopped
  • 2 cloves garlic, minced
  • 1/2 Tbsp fresh thyme
  • 1 tsp salt
  • 1/4 tsp black pepper
  • 1/2 cup Watusee Foods Chickpea Crumbs*
  • 2 Tbsp grated Parmesan**
  • 1 Tbsp butter, melted


  1. Preheat oven to 400 °F.
  2. Cut spaghetti squash in half lengthwise; remove inner seeds and stringy pulp. Spray insides lightly with olive oil-based cooking spray. Place cut-sides-down onto a foil-lined baking sheet, and bake for 30 minutes. Remove from oven to let cool. Keep oven on.
  3. Meanwhile, in a medium-sized bowl, whisk together eggs and yogurt. Stir in cheddar, onion, garlic, thyme, salt, and pepper.
  4. Once squash is cooled, lightly scrape flesh with a fork to remove all of the spaghetti-like strands from the skins. Add squash strands to egg mixture, and mix until well-combined. Pour squash mixture into a lightly-greased large casserole dish.
  5. Combine Watusee Foods Chickpea Crumbs, parmesan, and butter in a small bowl. Sprinkle over top of squash mixture, and press lightly with your fingers to moisten.
  6. Bake for an additional 30 minutes until beginning to brown. Optional (but highly recommended): Broil on low for 3 - 5 minutes to get the top a nice golden brown.


*Can substitute regular breadcrumbs.

**If you don't have Parmesan, use a little extra shredded cheddar.

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