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Overhead view of platter of pesto caprese spaghetti squash.

Caprese Spaghetti Squash

  • Author: Lexi
  • Total Time: 1 hour
  • Yield: 4 servings 1x
  • Diet: Vegan


This Pesto Caprese Spaghetti Squash with a bubbly mozzarella topping is a delicious vegan dinner or side dish! It's easy to make, packed with vibrant flavors and is naturally gluten free.


Units Scale

Spaghetti Squash:

  • 2 large spaghetti squash, cut in half lengthwise, seeds removed
  • 3 cups (~2 pints) cherry tomatoes, halved
  • 2 1/2 tablespoons olive oil, divided
  • 2 teaspoons balsamic vinegar
  • 1 1/2 teaspoon salt, divided
  • 3/4 teaspoon black pepper, divided
  • 1 cup Miyoko's Creamery Liquid Pizza Mozzarella, divided

Vegan Pesto:

  • 2 cups well packed basil leaves
  • 1/3 cup olive oil
  • 1/3 cup pine nuts, toasted
  • 2 tablespoons freshly squeezed lemon juice
  • 1/4 cup nutritional yeast
  • 2 cloves minced garlic
  • Salt and pepper to taste


  1. Preheat oven to 400˚F / 205˚C.
  2. Slice squash in half lengthwise and use a spoon to remove the seeds. Brush each half with 1/2 tablespoon of olive oil and sprinkle with 1/4 teaspoon of salt and 1/8 teaspoon of pepper. Set cut side down on baking sheet and roast for 35-40 minutes, until squash is fork tender.
  3. Remove squash from oven and let cool slightly before flipping over. Use two forks to shred the spaghetti squash and transfer the shredded squash to a large mixing bowl.
  4. While the squash is roasting, add basil, pine nuts, olive oil, lemon juice, nutritional yeast, garlic, salt and pepper to a food processor. Blend until mostly smooth. Taste and adjust seasoning as desired.
  5. In a skillet over medium heat, add the tomatoes, remaining 1 tablespoon of olive oil, balsamic vinegar, salt and pepper and stir well. Cook, stirring often, until tomatoes are softened and burst, about 6-8 minutes.
  6. Toss the shredded squash with pesto until well coated.
  7. Divide the squash + pesto mixture between the empty spaghetti squash skins. Top with tomatoes, then top each squash half with 1/4 cup of liquid mozzarella.
  8. Bake for 13-15 minutes (at 400˚F), or until cheese is bubbly and slightly browned. Remove from oven and serve warm with fresh basil.


How to make spaghetti squash easier to cut: If you're having trouble slicing the squash in half, poke several holes in the whole squash with a fork. Wrap in a damp paper towel and microwave on high for 3 minutes. Let cool slightly before cutting. This helps soften the squash so it's easier to cut, and also helps it cook faster in the oven.

Pine nuts: For maximum flavor, toast your pine nuts in a small skillet over low heat for a few minutes before adding to the pesto. Be careful – they burn quickly! You can also substitute pine nuts with pistachios, walnuts or pumpkin seeds.

Make this recipe faster: You can roast the spaghetti squash several days before using. You can also use store bought pesto instead of making it from scratch!

Storage: store leftovers in an airtight container in the refrigerator for 3-4 days. Reheat in the microwave or the oven.

  • Prep Time: 40 minutes
  • Cook Time: 20 minutes
  • Category: Dinner
  • Method: Oven
  • Cuisine: American


  • Serving Size:
  • Calories: 425
  • Sugar: 5.4 g
  • Sodium: 1297.1 mg
  • Fat: 36.7 g
  • Carbohydrates: 14.9 g
  • Fiber: 5.2 g
  • Protein: 14.5 g

Keywords: caprese spaghetti squash