Healthy Spaghetti Squash Pizza Bake

Wait until you try this delicious, healthy spaghetti squash pizza bake! I know pizza is one of your favorites! This family-friendly spaghetti squash pizza casserole is a low-carb comfort food that will become a new favorite for you and your family.

My healthy pizza spaghetti squash bake can please everyone. It tastes like super yummy pizza, but it’s loaded with vegetables and protein. It’s gluten-free and grain-free, and it can be tweaked to please picky eaters or spiced up for more adventurous eaters. It’s even delicious if you want to make it vegetarian style.

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Spaghetti squash
Spaghetti squash

Prepping the Spaghetti Squash

Have you cooked a spaghetti squash before? It’s a little tricky until you get the hang of it.

First you need to wash your spaghetti squash. It’s been all over the place and who knows who has touched it. I spray mine with Veggie Wash, rub it all over with my hands, and give it a good rinse.

I recently have gotten good at cooking my spaghetti squash in the microwave. Turns out it’s much faster and easier than in the oven!

I just prick it all over with a fork or small knife, and then put it in the microwave for 10 minutes. When I take it out (with potholders – it’s hot!) I put it on a cutting board. I’m then able to cut it in half lengthwise with a large knife. Careful – watch out for the steam!

I give it a few minutes to cool down, and then I can scoop out the seeds in the middle with a large spoon. Next, I take a fork and check to see if I can get the strands of the spaghetti squash to separate. If so, I’m good to go! I use the fork to get the strands out and put them into a large bowl.

If they’re not separating, then I put half of the squash back into the microwave for one minute and then I try again. Careful not to overcook it – you don’t want the strands to turn mushy.

If you’d rather cook your spaghetti squash in the oven instead of the microwave, you can see my instructions for that in my recipe for Spaghetti Squash Lazy Lasagna.

Spaghetti squash
Separate the spaghetti squash’s strands with a fork

Get Your Spaghetti Squash Pizza Toppings Ready

What are your favorite pizza toppings? Whatever you like on your pizza can go in your spaghetti squash pizza bake. My family loves Italian sausage, pepperoni, and olives the best, so that’s what I’ve included. But you can add mushrooms, green onions, artichokes, sun dried tomatoes – whatever you like.

I like to use bulk Italian sausage, either pork or chicken. You can also buy the links and squeeze the raw sausage out. If you are using any of these types of Italian sausage, then you need to cook it before you put it in the pizza casserole. So I get that started while my spaghetti squash is cooking. I also add in a chopped onion, and when the sausage is getting close to being cooked all the way through I turn down the heat and add a few cloves of crushed garlic.

You could also use ground beef if you prefer, or even ground turkey. If you use plain meat, I would add some salt, pepper, and garlic powder. Italian seasoning or a little dried basil or oregano would be good, too. Or you could use fully cooked Italian sausage links. If you do that, just cut it up first and saute it a bit to warm it up and brown it a little.

If your family likes mushrooms on their pizza, add them in now and precook them a bit, too.

Mixing the Spaghetti Squash Pizza Bake Together

Now take the scooped spaghetti squash strands and cooked meats and vegetables and mix them all together (you are going to need either a really big bowl or a really big pan).

Add in a jar of pizza sauce, a can of sliced olives (if you’re using them), and whichever other toppings your family likes. I also add in about 3 ounces of chopped pepperoni at this point (I quarter the regular-sized slices). I also add some salt, pepper, and dried basil or Italian seasoning.

Prep a 9 x 13 baking pan with a bit of cooking spray, and then dump the whole mixture into the pan.

Whisk up 4 eggs and 1/4 cup cream in a small bowl and pour it over the top. Mix it in a bit so you don’t see the eggs anymore.

Sprinkle mozzarella cheese all over the top, and then add on the last ounce of pepperoni. You could also decorate it with some olives or other toppings on top, if you like.

Bake at 400 degrees Fahrenheit for an hour.

Serve with a salad, maybe some French bread for the kids, and a nice big glass of red wine for you!

Easy Alterations for Spaghetti Squash Pizza Bake

It would be no problem to make this vegetarian! Simply leave out the meat and add in some extra vegetarian toppings – maybe some bell peppers?

Vegan wouldn’t work so well as you’d have to leave out the eggs and cheese – then it would no longer be high in protein. Your kids need the healthy protein and fats – don’t do that.

If you have just one or two vegetarians in your family, it would work great to make it without the sausage and then cook the sausage and pepperoni on the side and sprinkle it over the top for those who want it. Just as yummy, and can please the whole crowd!

It’s already gluten and grain free, so you are good to go, there!

If you want it to be paleo, you’ll have to leave out the cheese and cream. That’s super sad, but I’ll support you. It will still be tasty.d

If you’re keto, this should pretty much fit the bill. Just make sure you are using a low-sugar pizza sauce, and don’t use sundried tomatoes.

Here are some of the products I like to use in my spaghetti squash pizza bake recipe:

Spaghetti squash pizza bake

Spaghetti Squash Pizza Bake

Spaghetti Squash Pizza Bake is a super yummy low-carb comfort food! It's loaded with protein, veggies, and flavor. It's easy to customize for picky eaters and different eating needs.
Prep Time 30 minutes
Cook Time 1 hour
Resting time 10 minutes
Course dinner
Cuisine American, Italian
Servings 8


  • 1 large spaghetti squash
  • cooking spray – olive oil or avocado oil
  • 2 lb Italian sausage
  • 1 onion, chopped
  • 3 cloves garlic, crushed or chopped
  • 1 16 oz jar of pizza sauce
  • 4 oz pepperoni, divided
  • 1 2 oz can of sliced olives
  • 2 tsp dried basil or Italian seasoning
  • salt and pepper to taste
  • 4 eggs, whisked
  • 1/4 cup heavy cream
  • 12 oz shredded mozzarella cheese


  • mushrooms, peppers, sundried tomatoes, artichoke hearts, green onions, etc.


  • Preheat the oven to 400 degrees Fahrenheit. Spray a 9 x 13 baking pan with cooking spray
  • Wash and dry spaghetti squash. Pierce all over with a fork or small knife. Cook in microwave for 10 minutes.
  • When spaghetti squash is done, carefully take it out of microwave with potholders. Place on a cutting board. Using a large knife, cut it in half lengthwise. Careful of the steam!
  • Scoop out the seeds with a large spoon. Using a fork, check to see if the strands will separate into threads. If not, microwave each half an additional minute at a time, checking after each minute. Do not overcook. Mushy strands are not what you want.
  • Once the squash is cooked, let it cool for about 10 minutes. Then using a fork, scrape the strands out into a large bowl. You may need a large spoon to get the last bits out.
  • While the spaghetti squash is cooking, heat a large pan on the stove over medium high heat. Add the sausage and chopped onion (and mushrooms if using). Cook and crumble the sausage until cooked through. When it's almost done, turn the heat down to low and add the garlic to the pan. Cook for another minute, careful not to brown the garlic.
  • In a very large bowl or pan, mix together the spaghetti squash strands and the meat mixture. Add the pizza sauce, 3 ounces chopped pepperoni, olives, dried basil or Italian seasoning, and salt and pepper to taste. Add in any other optional ingredients. Mix well. Pour into prepared pan.
  • In a small bowl, whisk together the eggs and cream. Pour this over the spaghetti squash mixture and mix a bit until the eggs aren't showing.
  • Sprinkle cheese over the top. Decorate the top with the last ounce of pepperoni (and anything else you want).
  • Bake in 400 degree oven for an hour, until eggs are cooked through.
  • Let rest for 5-10 minutes before serving so it sets up a bit.
Keyword baked, casserole, easy, family-friendly, garlic, gluten-free, grain-free, healthy, low-carb, protein

Looking for more family-friendly low-carb recipes like this? You might also like:

Low-Carb Spaghetti Squash Lasy Lasagna

Family-Friendly Cheeseburger Casserole

Jalapeno Popper Chicken Skillet

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