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Home » Recipes » Vegan Main Dishes

Caprese Spaghetti Squash

Published: Jan 26, 2022 · Modified: Jan 26, 2022 by Lexi

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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.

This post is sponsored by Miyoko's Creamery. All opinions are our own.

Overhead view of platter of pesto caprese spaghetti squash.
Jump to:
  • 🥗 Why We Love This Recipe
  • 🍅 Ingredients
  • 📋 Ingredient Notes
  • 🧀 The Key Ingredient
  • 🔪 Step-by-step Instructions
  • 💭 Expert Tips and FAQs
  • 🍽 Related Recipes
  • 📖 Recipe
  • 💬 Reviews

🥗 Why We Love This Recipe

  • Packed with flavor: Roasted spaghetti squash is tossed with homemade pesto and topped with pan-roasted balsamic cherry tomatoes and the creamiest vegan mozzarella. It's baked to perfection and every bite is absolutely delicious!
  • Easy weeknight dinner: This caprese spaghetti squash comes together in just a few steps. Plus, you can make it even faster by roasting the squash ahead of time and using store-bought pesto.
  • Vegan and gluten free: This caprese spaghetti squash is perfect for just about any dietary needs!

🍅 Ingredients

Here's what you'll need to make this caprese spaghetti squash:

overhead view of ingredients for caprese spaghetti squash in prep bowls.

📋 Ingredient Notes

  • Spaghetti squash: Choose relatively large (wide) spaghetti squash for this recipe – you want something that's big enough for adding filling.
  • Tomatoes: We used cherry tomatoes, but grape tomatoes or even campari tomatoes work well in this recipe. You can also used diced roma tomatoes.
  • Nutritional yeast:  Nutritional yeast (aka "nooch") is an inactive form of yeast that has a buttery, cheesy flavor and is an excellent source of B vitamins. This is what we use in our homemade vegan pesto in place of parmesan cheese. It's easy to find in just about any grocery store and comes in handy for so many vegan recipes!
  • 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!
    • Pine nuts can be pretty expensive, but luckily you can sub them with another less expensive nut or seed! A few of our favorites include pistachios, walnuts or pumpkin seeds. It's not traditional for pesto, but it will still work.
  • Balsamic vinegar: you can also use balsamic reduction. We also like to drizzle a bit more over the top of each squash before serving.

🧀 The Key Ingredient

If you haven't yet heard about Miyoko's Creamery Liquid Vegan Pizza Mozzarella, you're in for a treat!

side view of Miyoko's Liquid vegan pizza mozzarella bottle.

Miyoko's is seriously revolutionizing the vegan cheese industry with this new product. We first tried it last summer and we're totally hooked!

Vegan cheese can have a bad rap when it comes to melting. Miyoko’s came up with the brilliant idea to make a liquid cheese by removing all the ingredients that hinder performance (did you know most shreds contain things like caking agents to keep shape?!) and cutting straight to the melt. It tastes just the same, but actually gets melty, bubbly, and seriously cheesy!

It's INCREDIBLE on homemade pizza and all sorts of other baked dishes, like lasagna, enchiladas, casseroles, hot dips, baked pasta, and of course, this caprese spaghetti squash!

We also love that it's made from plant milk (ethically sourced cashews) and is palm oil free.

Miyoko's Creamery is a mission driven, woman-founded brand and we're constantly so impressed by their incredibly high quality products. They're truly changing the food industry as a whole and we're such huge fans! You can see where to find their products here, or order online here.

close up view of pesto caprese spaghetti squash and Miyoko's Liquid vegan pizza mozzarella bottle.

🔪 Step-by-step Instructions

PREP: Preheat oven to 400˚F / 205˚C. 

(1) Slice squash in half lengthwise and use a spoon to remove the seeds. Brush each half with ½ tablespoon of olive oil and sprinkle with ¼ teaspoon of salt and ⅛ teaspoon of pepper. Set cut side down on baking sheet and roast for 35-40 minutes, until squash is fork tender. 

(2) 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. 

Before and after roasting spaghetti squash on a sheet pan.

(3) 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. 

(4) Toss the shredded squash with pesto until well coated. 

on the top: pesto in food processor. on the bottom: pesto mixed with spaghetti squash.

(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. 

Before and after pan roasting tomatoes.

(6) Divide the squash + pesto mixture between the empty spaghetti squash skins. Top with tomatoes, then top each squash half with ¼ cup of liquid mozzarella. 

stuffing spaghetti squash with pesto, tomatoes and mozzarella cheese before baking.

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. 

💭 Expert Tips and FAQs

  • 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.
  • Use tongs when handling the spaghetti squash after it comes out of the oven. It stays super hot for quite a while and it's easy to burn yourself, so we recommend using tongs when shredded the squash.
  • 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.
  • For extra caprese flavor, serve with a drizzle of balsamic vinegar or balsamic reduction.
  • Additions: Feel free to add in extra vegetables with the tomatoes, like onion, broccoli, eggplant, zucchini, mushrooms, etc. It would also be great with artichokes, roasted red peppers or sun dried tomatoes.
  • Serve with: A protein of choice for a full meal. We love this Mediterranean grilled tofu, but just about any grilled or baked protein works well.
Close up view of pesto caprese spaghetti squash.

🍽 Related Recipes

  • close up side view of spaghetti squash filled with pesto, white beans and topped with breadcrumbs.
    Pesto Spaghetti Squash Boats with Mushrooms
  • Overhead view of arugula caprese salad in a bowl.
    Arugula Avocado Caprese Salad
  • Overhead view of spaghetti squash soup in a bowl.
    Spaghetti Squash Soup

Tried this recipe? Please leave a star ⭐️⭐️⭐️⭐️⭐️ rating below and/or a review in the comments section further down the page. You can also stay in touch with us through social media by following us on Instagram, Pinterest, and Facebook or by subscribing to our newsletter.

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📖 Recipe

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Overhead view of platter of pesto caprese spaghetti squash.

Caprese Spaghetti Squash


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5 from 1 review

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

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.


Ingredients

Units Scale

Spaghetti Squash:

  • 2 large spaghetti squash, cut in half lengthwise, seeds removed
  • 3 cups (~2 pints) cherry tomatoes, halved
  • 2 ½ tablespoons olive oil, divided
  • 2 teaspoons balsamic vinegar
  • 1 ½ teaspoon salt, divided
  • ¾ teaspoon black pepper, divided
  • 1 cup Miyoko's Creamery Liquid Pizza Mozzarella, divided

Vegan Pesto:

  • 2 cups well packed basil leaves
  • ⅓ cup olive oil
  • ⅓ cup pine nuts, toasted
  • 2 tablespoons freshly squeezed lemon juice
  • ¼ cup nutritional yeast
  • 2 cloves minced garlic
  • Salt and pepper to taste

Instructions

  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 ½ tablespoon of olive oil and sprinkle with ¼ teaspoon of salt and ⅛ 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 ¼ 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.

Notes

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

Nutrition

  • 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

Did you make this recipe?

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Comments

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  1. Jessica says

    January 03, 2025 at 8:01 am

    Very yummy!

    Things I did differently: I added zucchini to the tomatos and that was yummy, my husband mentioned a white bean would be good too! I agree.

    I am vegetarian and had parm and NY so I added half and half, I love a good homemade pesto, but didn’t want to omit parm. Also love the health benefits of NY.

    I used mozzarella pearls as I couldn’t find the myoki cream stuff and didn’t have time to go to Whole Foods. I wonder if mixing in some ricotta with the pearls could have been good? Didn’t need it. Just a thought,

    I never had cooked spaghetti squash before and prepped the morning of, I baked it for 35 and turned off the oven. The slow cool off period cooked it more and unfortunately it became very soft and mushy. Still tasted super yummy but didn’t have that spaghetti effect I was looking forward to. My bad! I’ve learned my lesson! Don’t over cook your squash!!

    Reply
  2. Rachel says

    May 02, 2022 at 7:33 pm

    Hi there, How much store-bought pesto would equal the amount needed for this recipe? Also, will shredded mozzarella work just as well?

    Reply
    • Lexi says

      May 02, 2022 at 7:36 pm

      Hi! You'll need a little over a cup (around 1 1/4 cups). And yes, shredded mozzarella will work just fine. Hope you enjoy!

      Reply
      • Rachel says

        May 05, 2022 at 10:59 am

        Thank you! Am making this on Saturday - will report back 🙂

Lexi and Beth toasting with wine.

Hi, we're Lexi and Beth, a mother-daughter team from Michigan. The recipes you'll find here are a reflection of how we bring our family together around the dinner table despite various dietary differences.

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