This delicious Spaghetti Squash Pizza Casserole is the perfect dish when you’re craving the flavors of pizza, but you want a healthier option. This recipe is not only dairy-free and gluten-free, but it is grain-free, low-carb, Whole30, paleo, and keto-friendly.

cooked spaghetti squash casserole in a white baking dish

Whether you’re doing a low-carb diet or just looking for an amazing way to use a spaghetti squash, this is the recipe you need!

I made it on whim and it’s become a regular weeknight meal in my household. It’s not that hard to make and everyone looks forward to eating it. Think of it as having the comfort of a cheesy pepperoni pizza, but it’s actually healthy comfort food.

Why You Need This Recipe

  • This spaghetti squash pizza casserole makes about five large servings. It’s perfect for a family, or for meal prepping for two people.
  • You can cook the spaghetti squash for this casserole up to several days in advance. Store the cooked squash in the refrigerator until you’re ready to make the casserole.
  • This pizza casserole recipe is entirely dairy-free, gluten-free, and grain-free! It is also low-carb, paleo, Whole30, and keto-friendly. Best of all, this delicious Spaghetti Squash Casserole tastes very similar to a pizza, but without the carbs or the mozzarella cheese.

Key Ingredients

labeled photo with ingredients for spaghetti squash pizza casserole

The ingredient list for this recipe is super basic.

  • Spaghetti squash is the star of this recipe. It provides structure for the casserole which mimics the texture of a real pizza.
  • Ground beef adds protein to the dish. I used grass-fed local beef but you could easily use ground turkey, Italian sausage, ground chicken, ground pork, or any other type of ground meat if you wish.
  • You’ll also need standard pizza ingredients including tomato sauce (or marinara sauce), seasonings, and pepperoni.
  • I also used eggs to help thicken the cooked spaghetti squash.

Please see the full recipe card below for the exact ingredients and measurements.

Recipe Steps

Step One

The first step for this healthy casserole is to cook a medium sized spaghetti squash.

My favorite method for this is to pop it in an Instant Pot pressure cooker at 15 minutes at high pressure. You can also make Crockpot Spaghetti Squash, or cut it in half and cook it in the oven.

No matter what method you use to cook your squash, you should end up with about 5 cups of cooked squash that is shredded and ready to use in the casserole.

Step Two

Preheat your oven to 400°F and spray a casserole dish with nonstick cooking spray. Don’t use a baking sheet for this recipe, you’ll need a dish.

In a large skillet, cook the beef, onion, and garlic. Then, add the tomatoes, spaghetti squash, and eggs, and then transfer the mixture to your baking dish.

spaghetti squash casserole process shot

Step Three

Top the spaghetti squash base with your pepperoni and olives, and bake it for 30 minutes.

If you aren’t dairy-free, you can certainly add cheese to the top as well for an even more authentic pizza experience. Or, you can use vegan cheese too.

You can also add your favorite pizza toppings, such as mushrooms, artichoke hearts, sautéed mushrooms, bell peppers, black olives, turkey pepperoni, pineapple, or whatever you prefer. Feel free to get creative!

Step Four

Once the casserole has baked through, it will start to turn a golden brown on top.

Remove it from the oven and let it cool for a few minutes before serving. Feel free to serve with fresh basil or red pepper flakes for aded flavor.

Use a sharp knife or a large serving spoon to serve.

I hope your whole family agrees that this delicious spaghetti squash pizza casserole is the perfect low-carb dinner.

slice of cooked spaghetti squash casserole

Recipe FAQs

Is this spaghetti squash casserole recipe healthy?

Yes, I think so! The casserole has a nice amount of protein and fat, while being very low in carbs.

Can this casserole be meal prepped?

Yes, it can! Prep this casserole up to 2 days in advance. Cover it with plastic wrap or a lid and store it in the refrigerator until you’re ready to bake it.

up close picture of spaghetti squash pizza casserole

More Healthy Casserole Recipes You Might Like

I hope you make this recipe! If you do, please leave a comment and a starred review below.

And, consider following me on social media so we can stay connected. I’m on Facebook, Pinterest, Instagram, and YouTube!

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pizza casserole in a white baking dish ready to be served

Spaghetti Squash Pizza Casserole (Dairy-Free)

5 Stars 4 Stars 3 Stars 2 Stars 1 Star

5 from 1 review

This delicious Spaghetti Squash Pizza Casserole is the perfect dish when you’re craving the flavors of pizza, but you want to have a healthier option. This recipe is not only dairy-free and gluten-free, but it is grain-free, low-carb, Whole30, paleo, and keto-friendly.

  • Total Time: 45 minutes
  • Yield: 5 1x


Units Scale
  • Nonstick cooking spray
  • 1 pound lean ground beef
  • 1/2 onion, chopped
  • 2 garlic cloves, minced
  • 5 cups cooked and shredded spaghetti squash, from about 1 medium spaghetti squash
  • 1 cup chopped or crushed tomatoes, with the juice
  • 1 teaspoon ground oregano
  • 2 eggs, beaten
  • 34 ounces, pepperoni slices
  • 1/4 chopped black olives


  1. Preheat your oven to 400°F. Spray a casserole dish with nonstick cooking spray and set aside.
  2. Heat a large skillet over medium heat. Add the ground beef, onion, and garlic, and use a spatula to break up the meat as it cooks.
  3. Cook the meat until it is just no longer pink, and then add the cooked spaghetti squash, chopped tomatoes, ground oregano, and eggs. Stir to combine the ingredients and then transfer them to the casserole dish. Use a spatula to flatten out the top of the casserole.
  4. Top the casserole with the pepperoni slices and olives and bake for 30 minutes, or until the top of the casserole starts to turn a golden brown.
  5. Remove the casserole from the oven and let it cool for a few minutes before serving.


  1. Cover the casserole dish if you have any leftovers and store it in the refrigerator for up to 4 days. Re-heat before serving.
  2. If you aren’t dairy-free, you can feel free to add shredded cheese on top of the casserole before baking. Or, you can always add a sprinkle of vegan cheese on top to keep the casserole dairy-free.
  3. You can also get creative with the toppings, using mushrooms or whatever you like on a pizza.


  • Serving Size: 1/5 of recipe
  • Calories: 280
  • Sugar: 5.7 g
  • Sodium: 468.2 mg
  • Fat: 13.3 g
  • Saturated Fat: 5.1 g
  • Carbohydrates: 12.9 g
  • Fiber: 2.8 g
  • Protein: 27.4 g
  • Cholesterol: 145.1 mg

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About the Author: Carrie Forrest has a master’s degree in public health with a specialty in nutrition. She is a top wellness and food blogger with over 5 million annual visitors to her site. Carrie has an incredible story of recovery from chronic illness and is passionate about helping other women transform their health. Send Carrie a message through her contact form.