Roasted spaghetti squash, fresh basil pesto, roasted tomatoes and mozzarella cheese are all combined in this delicious Caprese Spaghetti Squash recipe! It’s healthy, gluten free and easy to make in under an hour.

roasted spaghetti squash filled with tomatoes and mozzarella cheese

This recipe is one of my favorite ways to use spaghetti squash. Roasted cherry tomatoes are bursting with natural sweetness, while the strands of spaghetti squash are tossed with flavorful basil pesto and the dish is finished off with creamy, melted mozzarella cheese. This combination of flavors can not be beat!

If you’re new to cooking with spaghetti squash, get ready to fall in love with this simple, gluten free alternative to pasta. Spaghetti squash is very low in calories and packed with vitamins, minerals and fiber.

If you’re already a fan, get ready to enjoy a whole new way to eat this delicious squash. Caprese Spaghetti Squash is bursting with flavor, low in calories and carbs, and gluten free, a winning combination! I usually eat this recipe for dinner, but it could also be served as a side dish with Italian favorites like Three Cheese Manicotti, Beef Ragu or Italian Meatballs.

Table of contents

caprese spaghetti squash ingredients

Ingredients

  • Spaghetti squash – look for a medium-sized squash that’s about 4 pounds in size, this will yield approximately 5 cups of spaghetti squash strands. Check out this guide for how to cook spaghetti squash in the microwave, oven or air fryer. If you’re short on time, the microwave is a great option to make this recipe in under 30 minutes!
  • Olive oil – or another neutral oil of your choice, like avocado oil or sunflower oil.
  • Basil pesto – click the link for my easy homemade pesto recipe. You can also purchase pre-made pesto at the grocery store. Rana is our favorite store-bought brand, and it’s available in the refrigerator, usually near the deli section of the grocery store.
  • Cherry tomatoes – or grape tomatoes will also work.
  • Garlic cloves
  • Balsamic vinegar
  • Mozzarella cheese – you can use fresh mozzarella cheese, diced into cubes, like I did in this recipe, or use shredded mozzarella cheese. I’ve used both in this recipe over the years, and they both work great!
  • Salt and pepper – used to season the spaghetti squash and roasted cherry tomatoes.
cut spaghetti squash on baking stone
Caprese Spaghetti Squash Recipe

Instructions

  1. Prepare the squash. Cut the spaghetti squash in half lengthwise and remove the seeds. Then, brush with olive oil and sprinkle with salt and pepper.
  2. Bake the squash. Place the squash cut side down on a rimmed baking sheet and roast in the oven at 400°F for 30-45 minutes. A 4 pound squash should only take 30 minutes to roast, while a 5-6 pound squash will take 45 minutes.
  3. Roast the veggies. On a separate baking sheet lined with foil, add the cherry tomatoes and garlic. Drizzle with olive oil and balsamic vinegar. Sprinkle with salt and pepper. After the squash has been roasting for 10 minutes, place the tomatoes in the oven to roast for the remaining 20 minutes.
  4. Cool it down. Remove both the spaghetti squash and tomatoes from the oven. Set the tomatoes aside. Allow the squash to cool slightly.
  5. Make the noodles. Use a fork to pull the spaghetti squash strands into “noodles” and place them in a large bowl.
  6. Mix in the sauce. Add the pesto to the squash and toss until all of the noodles are coated.
  7. Finish the dish. Turn the oven broiler on to high. Stuff the pesto squash back in the shells, add the roasted cherry tomatoes and mozzarella cheese. Place on a baking sheet and into the oven under the broiler for 2-3 minutes, or until the cheese is melted. Remove from the oven and finish with a few fresh basil leaves and fresh grated parmesan cheese, if you’d like.
roasted spaghetti squash stuffed with tomatoes, basil and mozzarella

Frequently asked questions

  • How do you make spaghetti squash not watery? To avoid a watery squash, sprinkle with salt before cooking to draw out the extra moisture, and roast the halves cut side down.
  • Is spaghetti squash healthy? Yes! Spaghetti squash is a filling low calorie food with only half a gram of fat per cup. It’s low in carbs and rich in antioxidants, plus it’s a great source of fiber, which helps with digestive health. It’s a great healthy alternative to traditional spaghetti noodles.
  • How do you cut a spaghetti squash in half? If you’re having a hard time cutting the spaghetti squash in half before roasting, I recommend using an electric knife. If you don’t have an electric knife, put the whole spaghetti squash in a 400°F oven for 10 minutes. Remove it from then oven, then use a sharp knife to slice it in half once it’s cool enough to touch. Starting the cooking process slightly will help soften the outside of the squash and make it easier to cut in half.

Storing and reheating

Store any leftovers in an airtight container in the refrigerator for up to 5 days. You can reheat the caprese spaghetti squash in the microwave or the oven.

To reheat in the microwave, place it on a microwave-safe plate and microwave for 2-3 minutes. To reheat in the oven, place the squash on an oven-safe pan and into a 350°F oven for 10-15 minutes, or until heated throughout.

roasted spaghetti squash filled with roasted cherry tomatoes and melted mozzarella cheese

More spaghetti squash recipes

Get more healthy spaghetti squash recipes in your life with these tasty dishes!

roasted spaghetti squash filled with roasted tomatoes and melted mozzarella cheese
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Caprese Spaghetti Squash

Roasted spaghetti squash, fresh basil, roasted tomatoes and mozzarella cheese are all combined in this delicious Caprese Spaghetti Squash recipe! It's healthy, gluten free and easy to make in under an hour.
Servings: 4 people
Prep Time: 15 mins
Cook Time: 30 mins
Total Time: 45 mins
Author: Whitney Bond
Course: Main Course
Cuisine: Italian

Ingredients

  • 4 pound spaghetti squash
  • 4 tablespoons olive oil, divided
  • 1 teaspoon kosher salt, divided
  • 1 teaspoon black pepper, divided
  • ¼ cup basil pesto
  • 2 cups cherry tomatoes
  • 4 cloves garlic
  • 1 tablespoon balsamic vinegar
  • ¼ cup fresh mozzarella cheese, diced

Instructions

  • Preheat the oven to 400°F.
  • Cut the spaghetti squash in half lengthwise, remove the seeds and brush with 1 tablespoon olive oil, then sprinkle with ½ tsp salt and ½ tsp black pepper.
  • Place the squash cut side down on a baking sheet and roast in the oven for 30 minutes. Note that a larger squash, 5-6 pounds in size, will take 45 minutes to roast.
  • On a separate baking sheet lined with foil, add the cherry tomatoes and garlic.
  • Drizzle with the remaining 3 tablespoons olive oil and 1 tablespoon balsamic vinegar.
  • Sprinkle with the remaining ½ teaspoon salt and ½ teaspoon black pepper.
  • After the squash has been roasting for 10 minutes, place the tomatoes in the oven to roast for the remaining 20 minutes.
  • Remove both the spaghetti squash and tomatoes from the oven.
  • Set the tomatoes aside.
  • Allow the squash to cool slightly then use a fork to pull the spaghetti “noodles” from the squash and into a large bowl.
  • Add the pesto to the squash and toss to coat.
  • Turn the oven broiler on to high.
  • Stuff the pesto squash back in the shells, add the roasted cherry tomatoes and mozzarella cheese.
  • Place on a baking sheet and into the oven under the broiler for 2-3 minutes, or until the cheese is melted.
  • Remove from the oven and finish with a few small basil leaves and fresh grated parmesan cheese, if you’d like.

Notes

  • Store any leftovers in an airtight container in the refrigerator for up to 5 days
  • To reheat the squash in the microwave, place it on a microwave-safe plate and microwave for 2-3 minutes.
  • To reheat the squash in the oven, place the squash on an oven-safe pan and into a 350°F oven for 10-15 minutes, or until heated throughout.
  • If you’re having a hard time cutting the spaghetti squash in half before roasting, I recommend using an electric knife. If you don’t have an electric knife, put the whole spaghetti squash in a 400°F oven for 10 minutes. Remove it from then oven, then slice it in half once it’s cool enough to touch. Starting the cooking process slightly will help soften the outside of the squash and make it easier to cut in half.

Nutrition Facts

Serving 2gCalories 345kcal (17%)Carbohydrates 28g (9%)Protein 6g (12%)Fat 25g (38%)Saturated Fat 5g (25%)Polyunsaturated Fat 2gMonounsaturated Fat 11gCholesterol 9mg (3%)Sodium 860mg (36%)Potassium 539mg (15%)Fiber 6g (24%)Sugar 12g (13%)Vitamin A 1114mg (22%)Vitamin C 25mg (30%)Calcium 127mg (13%)Iron 2mg (11%)
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