Low Carb Spaghetti Squash and Meatballs with Fresh Mozzarella

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This low carb spaghetti squash and meatballs with fresh mozzarella is the ultimate comfort food. Flavor-packed beef meatballs and tender spaghetti squash noodles all tossed in a quick homemade marinara. You won't miss the spaghetti at all!

416 CAL 36g CARBS 16g FAT 36g PROTEIN

Missing Italian food lately? Enjoy a plate of classic comfort food (with fewer carbs) like my version of Spaghetti Squash and Meatballs recipe! It's a healthy dinner that tastes just as good as it looks (and you won't even miss the pasta!).

This delicious recipe for low-carb spaghetti squash with meatballs is made with fresh mozzarella and definitely fits the bill when you want a comforting home-cooked meal. What's better about this dish is that this is actually a spaghetti and meatball dish you can feel good about.

It's made with simple and healthy ingredients and packed with veggies. It all starts with roasted spaghetti squash replacing traditional pasta. Then, the spaghetti is topped off with a tasty marinara sauce and mozzarella cheese.

When you are craving pasta, this recipe is the perfect replacement. In fact, you might start wanting to make this instead of pasta - it really is that delicious!

Key Ingredients and Easy Swaps

These ingredients are super easy to find. In fact, you might already have most of them in your kitchen.

  • Spaghetti Squash: I used two spaghetti squashes and cut them in half vertically. You could swap in zucchini noodles or another veggie/low carb noodles. For a heartier dish, you could add soem regular spaghetti as well.
  • Oil: You need oil for the squash when you roast it in the oven. Either olive oil, ghee, or avocado oil will work perfectly for this purpose.
  • Garlic: Fresh garlic cloves have the most flavor. Since you are using them in the spaghetti sauce, I definitely suggest using fresh cloves over dried powder.
  • Onion: Either yellow or white onion tastes better in spaghetti sauce. To save yourself time, you can also use frozen diced onion.
  • Tomatoes: A can of crushed tomatoes is the easiest way to make homemade marinara sauce. It's healthy and a time-saver. Swap in a store bought marinara or spaghetti sauce if you prefer.
  • Spices: There are two places you will use the spices - in the sauce and the meatballs. Use your favorite Italian herbs for both! I used parsley, basil, and oregano.
  • Meat: For the meatballs, use your favorite type of meat. I used ground beef, but you can make turkey meatballs too.
  • Cheese: You'll need parmesan cheese for the meatballs and fresh mozzarella on top of the spaghetti squash at the end. You could swap in pecorino romano cheese as well and use shredded mozzarella on top.
  • Egg: Always use an egg to bind meatballs together. Otherwise, they will fall apart.

Note: For a full list of ingredients and detailed instructions on how to make this recipe, take a look at the printable recipe card at the bottom of this post!

What’s the best way to cook spaghetti squash?

There are many ways to cook spaghetti squash and it mostly will depend on how much time you have.

For best results, I recommend roasting the spaghetti squash since it brings out the most flavor, but the microwave also works for a faster option.

  • Oven roasted: Preheat the oven to 400 degrees. Cut the squash in half lengthwise and remove the seeds. Brush with olive oil and roast with te cut side down for 40-50 minutes until tender.
  • Microwave: Pierce the entire squash all over with a fork or knife. Place on a microwave safe dish and microwave for 10-15 minutes until tender to the touch. Carefully open and remove the seeds.
  • Stovetop: Cut the squash into 6-8 pieces, removing the seeds. Place in boiling water and cook for 10-15 minutes until tender.
  • Instant Pot: Slice the squash in half lengthwise and remove the seeds. Place in a steamer basket in the Instant Pot with 1 cup of water. Cook for 7 minutes and let naturally release.

Recipe Tips And Ideas

Follow these tips to make sure that this spaghetti squash turns out perfectly every single time!

  • Add olive oil to the spaghetti squash or spray with cooking spray. This will help it cook and become nice and tender without burning.
  • Simmer your meatballs in the sauce. The fresh herbs and rich tomatoes will perfectly coat the meatballs, infusing them with the taste.
  • For a really crispy top, broil the spaghetti squash after you add all the sauce and cheese inside.
  • Add extra veggies! Wilt some spinach into the sauce for even more veggies or saute some zucchin to add to the final dish.

What To Serve With Spaghetti Squash With Meatballs

This is a classic Italian recipe, so serve some of your favorite side dishes with it. You could have some caprese flatbread on the side - it only takes 10 minutes and has fresh basil and mozzarella, just like in your spaghetti squash.

Then, all you need is this healthy kale Caesar salad with your spaghetti squash and meatballs, and you have a full meal ready to go!

This dish also works really well with a bright Arugula Salad or Cucumber Salad.

Frequently Asked Questions

Here are some questions I frequently get asked about by some readers...

How do you make this Whole30 or Paleo-friendly?

If you are on the Whole30 or Paleo diet, the only thing you need to change in this recipe is the cheese. Leave out the cheese, and this is a Whole30 and Paleo-compliant meal that's still just as delicious.

How can I save time and prep this ahead of time?

Since this recipe takes a little longer to prepare, consider prepping it during the weekend so you can assemble it quickly midweek. Just make up the meatballs and sauce on the weekend.

Instead of roasting your spaghetti squash, pierce it with a fork and put it in the microwave for 10 to 12 minutes until it's soft. When tender, cut your squash carefully in half, and remove the seeds.

Next, add the meatballs, sauce, and cheese and pop it under the broiler until everything is browned and melted. Easy, peasy!

How do you store leftover spaghetti squash?

The best way to store leftovers is to scrape out the spaghetti squash and layer it in an airtight dish with marinara sauce and meatballs. It will stay fresh in the refrigerator for about 5 days if it is tightly sealed.

What are other pasta alternatives?

There are lots of other healthy alternatives to pasta. Zucchini noodles (or zoodles) are one of my favorite ways to enjoy an alternative to pasta. Another popular choice is Palmini noodles which are low-carb and made from the hearts of palm. You'll find them in a can at most popular grocery stores.

More Delicious Spaghetti Squash Recipes You’ll Love:

The Recipe
Spaghetti squash and meatballs with marinara sauce and melted fresh mozzarella cheese.

Low Carb Spaghetti Squash and Meatballs with Fresh Mozzarella

416 CAL 36g CARBS 16g FAT 36g PROTEIN
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  • 2 spaghetti squash, halved
  • 2 tsp olive oil
  • 4 cloves garlic, minced
  • 1/2 onion, diced
  • 28 oz. canned crushed tomatoes
  • 1 bay leaf
  • 1/2 tsp oregano
  • 1 lb. 95% lean ground beef (or turkey)
  • 1/4 cup Parmesan cheese
  • 1/4 cup parsley, minced
  • 1 egg
  • 1 garlic clove, minced
  • 1 tsp. salt
  • 1 tsp. pepper
  • 2 oz. fresh mozzarella
  • 1/4 cup basil, chopped

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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.


Meanwhile, heat the olive oil over medium heat in large sauce pan. Add the onion and garlic and cook for 4-5 minutes. Add the crushed tomatoes, bay leaf, and oregano. Bring to a simmer and cover.


Combine the beef, Parmesan cheese, parsley, egg, garlic, salt, and pepper in a bowl. Form into one inch meatballs and drop into the tomato sauce.


Simmer the meatballs for 20 minutes until cooked through.


To assemble spaghetti squash boats, first scrape the spaghetti squash away from the edges using a fork. Add the meatballs and some of the tomato sauce. Layer thin slices of mozzarella on top. Return to oven and cook for 3-5 minutes until cheese melts. Top with basil.

Nutritional Facts
Serving Size: 1/2 spaghetti squash with 3 meatballs
Amount Per Serving
Calories 416
Calories from Fat 95
% Daily Value *
Total Fat 16g
Saturated Fat 7g
Monounsaturated Fat 2g
Polyunsaturated Fat 0g
Cholesterol 133mg
Sodium 1126mg
Total Carbohydrate 36g
Dietary Fiber 8g
Sugars 17g
Protein 36g

* 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
On Low Carb Spaghetti Squash and Meatballs with Fresh Mozzarella
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September 17, 2022 - 13:22
Haven’t made this yet but looks yummy. When you say 1/2 of the squash does that mean 1 full half??
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October 4, 2022 - 18:37
Yes! This is a rather large serving with 1/2 squash for each serving.
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Darlene H
January 22, 2019 - 16:00
This was a delightful meal and recipe. We loved it! Simple, lots of good fresh taste, and overall a great meal. I rate it 5 stars!!!
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October 13, 2018 - 11:48
A must try
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Milissa Bergman
January 31, 2017 - 06:46
Add a Rating:
Love this recipe! It's so quick and easy. Even my husband, (who hates squash) likes it!
Great for a quick weeknight meal.
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Carrie Drissi
February 8, 2016 - 14:44
Add a Rating:
I am beginning to LOVE this site! very recipe I've tried for the past week have been outstanding including this one. My teenage boys wanted more.
The smart points I calculated for this recipe using the recipe builder on the ww site are only 6 points per serving. So I added a touch more freshly grated parm to top mine off to make up for the extra point.
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Marise Rowell
January 3, 2016 - 18:35
Add a Rating:
This is the first SK recipe I've tried and I must say I'm impressed! Not nearly as challenging as I first expected and also delicious and filling. My 13-year-old even liked it, and I have enough leftover meatballs and sauce for the freezer.
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