Italian Spaghetti Squash Casserole

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Italian Spaghetti Squash Casserole is a healthy and filling low carb dish packed with a homemade bolognese, spaghetti squash, and fresh mozzarella.

370 CAL 24g CARBS 16g FAT 34g PROTEIN
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Italian Spaghetti Squash Casserole is a delicious, low carb alternative to baked pasta dishes that are made with tender spaghetti squash, a homemade meat sauce, and fresh mozzarella.

Spaghetti squash has been a mainstay in my diet for years now and I am happy to report I am finally beginning to get the whole family to enjoy it. In the past, I would usually make a pasta dish using spaghetti squash for me and regular pasta for everyone else. Sometimes I would sneak some spaghetti squash into their pasta to add extra veggies, but many times I would just prepare the sauce separately so I could easily make both.

Last week I had a rare night home alone and decided to make this spaghetti squash casserole since I was craving baked pasta and let's be honest, cheese. Instead of ordering out for a calorie bomb, which was definitely a temptation as I contemplated a night of Netflix, pasta, and wine; I decided to make a healthier version at home.

This meant I could still enjoy my relaxing evening - just without the guilt. So I whipped together a quick bolognese, threw my spaghetti squash in the microwave for quick cooking, and then tossed everything together with some fresh mozzarella and baked it in the oven. Then happily sank into the couch and relished my quiet evening at home alone. It was amazing.

Then the next day to my surprise, when I pulled out my leftovers for lunch, everyone was interested in trying them. I think it's because it looked so much like the baked pasta I sometimes make. They were all shocked to learn it was only spaghetti squash and even more surprised that they liked it. Luckily, I had made a big batch so there was plenty to go around.

Italian Spaghetti Squash Casserole with Fresh Mozzarella.

Can I make spaghetti squash casserole with chicken? turkey? sausage?

Sure! This casserole can be made with virtually any protein you like. Ground beef, ground turkey, and ground chicken all work. You can also use ground or sliced chicken or turkey sausage. Another option is to use chicken breast. Simply shred or chop the chicken breast and toss it with the spaghetti squash before baking it.

How to Cook Spaghetti Squash

There are lots of ways you can cook your spaghetti squash for this casserole. It can also be prepped and cooked in advance for meal prep.

  • Microwave: Pierce the whole squash all over with a fork or sharp knife. Then place it on a microwave-safe plate and cook 10-15 minutes, until tender to the touch. Carefully remove it from the microwave, cut in half, and scoop out the seeds. It will be extremely hot, so if possible, let it cool before handling it.
  • Roasted: Cut the spaghetti squash in half and scoop out the seeds from the center. Drizzle with olive oil or spray with cooking spray. Season with salt and pepper. Then place the squash cut side down on a baking sheet and roast at 400 degrees for about 45 minutes or until it is tender.
  • Slow Cooker: Spaghetti squash can be cooked whole in the slow cooker. Simply pierce it using a fork or sharp knife. Then place it in the slow cooker with 1 cup of water and cook on low for 6-8 hours until tender.
  • Instant pot: Cut the spaghetti squash in half and remove the seeds. Add a steamer basket to the Instant Pot and place the squash on the steamer basket. Add 1 cup of water to the pot. Close and cook on Manual mode for 7 minutes. the seeds.

Low Carb Italian Spaghetti Squash Casserole in a skillet.

Tips for Making Italian Spaghetti Squash Casserole

  • Although I love the sweetness of spaghetti squash, this recipe would also work with cooked zucchini noodles. You could also throw in some cooked pasta if you wanted, but I guarantee you don't need it.
  • Personally, I love the creaminess of fresh mozzarella, but you can use any cheese you like. Regular shredded mozzarella, Parmesan, and even goat cheese would all be delicious.
  • If you can, try and buy crushed San Marzano tomatoes for this recipe. They are sweeter and less acidic than standard tomatoes and mean you will have a sweeter sauce without having to add any sugar.
  • Ground beef, turkey, chicken, sausage, or vegetarian crumbles are all options when it comes to protein for this dish. You could even use white beans for a natural, plant-based protein source.
  • If you need a shortcut, you can use jarred marinara sauce for this recipe. Just look for one with no added sugar that has the most natural ingredient list as possible.
  • For a Whole30 or Paleo spaghetti squash casserole, option, leave off the cheese.

Looking for more spaghetti squash dishes?

Italian Spaghetti Squash Casserole with a wooden spoon.

Here are some of the products and tools I used in creating this recipe:

  • Skillet: I am in love with this pan that I use to prepare this dish but you could use any heavy bottomed pan or cast iron.
  • Crushed San Marzano Tomatoes: If you can find San Marzano crushed tomatoes, I highly recommend using them as they will make a much better sauce than a traditional canned tomato since they are naturally sweeter and less acidic.
The Recipe
Spaghetti squash casserole with tomatoes, ground beef, and fresh mozzarella cheese.

Italian Spaghetti Squash Casserole

370 CAL 24g CARBS 16g FAT 34g PROTEIN
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  • 1 spaghetti squash (large)
  • 1 tbsp olive oil
  • 1/2 onion, minced
  • 1 carrot, diced
  • 1 celery stalk, diced
  • 4 garlic cloves, minced
  • 1 lb 95% lean ground beef
  • 16 oz. crushed tomatoes (ideally San Marzano)
  • 2 tbsp. tomato paste
  • 1 bay leaf
  • 4 cups spinach
  • 4 oz. fresh mozzarella
  • Salt and pepper

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Preheat the oven to 400 degrees. Cut the spaghetti squash in half and remove seeds. Spray with cooking spray and sprinkle with salt and pepper. Place cut side down on a baking sheet and bake for 35-40 minutes until tender. You can also microwave the spaghetti squash. Pierce it all over with a fork or sharp knife. Microwave for 10-15 minutes until tender to the touch. Carefully cut in half and scoop out the seeds. Then use a fork to scrape out the spaghetti squash.


Meanwhile, heat the olive oil over medium heat. Add the onion, carrot, celery, and garlic. Cook for 4-5 minutes until beginning to soften. Add the ground beef and cook for 4-5 minutes, breaking it up as you go, until it browns.


Add the crushed tomatoes, tomato paste, Italian seasoning, and bay leaf. Season with salt and pepper. Bring to a simmer and let simmer for 10 minutes. Stir in the spinach and cook for 1-2 minutes until it wilts.


Add the spaghetti squash and stir to combine. Taste and season if needed. In the same pan (or pour into a baking dish), top the spaghetti squash mixture with the fresh mozzarella. Bake in the oven for 10-15 minutes until mozzarella is melted. Serve with fresh basil if desired.

Nutritional Facts
Serving Size: 2 cups
Amount Per Serving
Calories 370
Calories from Fat 97
% Daily Value *
Total Fat 16g
Saturated Fat 7g
Monounsaturated Fat 2g
Polyunsaturated Fat 0g
Cholesterol 93mg
Sodium 396mg
Total Carbohydrate 24g
Dietary Fiber 7g
Sugars 12g
Protein 34g

* Percent Daily Values are based on a 2,000 calorie diet. Your daily values may be higher or lower depending on your calorie needs.

The Nutritional Values provided are estimates only and may vary based on the preparation method.

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About the author Meet Kristen McCaffrey
Hi, I’m the cookbook author, recipe developer, and food enthusiast behind Slender Kitchen. I am obsessed with making healthy food that is easy to prepare and absolutely delicious. Meal planning is my secret weapon and I hope I can make meal time easier for you with our tried and tested recipes and foolproof meal plans. Learn More
† We are a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for us to earn fees by linking to and affiliated sites.
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