Kalyn's Kitchen

Twice-Baked Spaghetti Squash with Pesto

Twice-Baked Spaghetti Squash with Pesto and Parmesan is a delicious idea that’s perfect for a low-carb meatless meal or side dish. 

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Twice-Baked Spaghetti Squash with Pesto in baking dish with plates and fork below

Are you a fan of spaghetti squash? It’s turned into a favorite fall vegetable for many people because it’s low in carbs, low in calories, and versatile. For years I grew spaghetti squash in my garden, and although I’m not especially a fan of it as a substitute for pasta, I love to eat it spaghetti squash a side dish or as the base of a bowl meal. And fall is when spaghetti squash shows up in the stores or Farmers markets, so I thought it was a good time to remind you about this ultra popular Twice-Baked Spaghetti Squash with Pesto

And spaghetti squash shows up in the garden about the time you’ve been making Pesto and storing it in the freezer, although if you don’t have any homemade pesto you can certainly use my favorite pesto in a jar for this recipe.

What ingredients do you need for this recipe?

  • spaghetti squash
  • Olive Oil (affiliate link)
  • Italian Herb Seasoning (affiliate link), or use other seasoning of your choice
  • Basil Pesto (affiliate link) (more or less to taste)
  • coarsely grated Parmesan cheese
  • salt and fresh ground black pepper

Want more spaghetti squash recipes?

Check out Spaghetti Squash Recipes for more ways to use this favorite fall vegetable

Do you love Pesto?

Check out Low-Carb and Keto Recipes with Pesto for more tasty ideas using basil pesto!

Twice-Baked Spaghetti Squash with Pesto and Parmesan found on KalynsKitchen.com

How to make Twice-Baked Spaghetti Squash with Pesto:

(Scroll down for complete printable recipe.)

  1. Cut spaghetti squash in half lengthwise and use a sharp spoon to scrape out the seeds and stringy gunk that’s around the seeds.
  2. Rub the cut sides with some olive oil and sprinkle with a little Italian Herb Seasoning (affiliate link).
  3. Roast the squash at 400F/200C until the squash pulls apart easily with a fork like this.
  4. I had a really big squash so I scraped it all out into a baking dish to mix the pesto and Parmesan with the squash. (You could do this in the same dish you bake it in if you’re not taking photos!)
  5. Here’s how it looked when the squash, pesto, and Parmesan was evenly mixed.
  6. I transferred it to this baking dish which is about 12 inches by 8 inches. Sprinkle with grated Parmesan.
  7. Bake 20-30 minutes more, or until it’s bubbling and starting to brown.
  8. Serve hot, with additional Parmesan to add at the table if desired.

Twice-Baked Spaghetti Squash with Pesto in baking sheet with plates and forks

More Meatless Ideas for Spaghetti Squash:

Mediterranean Spaghetti Squash with Vegetables and Feta ~ Kalyn’s Kitchen
Spaghetti Squash Tacos ~ Taste and Tell
Greek Salad Spaghetti Squash Bowl ~ Kalyn’s Kitchen
Cheesy Spaghetti Squash Marinara ~ Family Fresh Cooking
Spaghetti Squash and Black Bean Mexican Bowl ~ Kalyn’s Kitchen

Weekend Food Prep:

This recipe has been added to a category called Weekend Food Prep  to help you find recipes you can prep or cook on the weekend and eat during the week!

Twice-Baked Spaghetti Squash with Pesto

Twice-Baked Spaghetti Squash with Pesto

Yield 8 servings
Prep Time 15 minutes
Cook Time 1 hour 20 minutes
Total Time 1 hour 35 minutes

Spaghetti squash is delicious with pesto and Parmesan!


  • 1 large spaghetti squash (see notes)
  • 2 T olive oil
  • 2 tsp. Italian Herb Blend (or use other seasoning of your choice)
  • 3 T basil pesto (more or less to taste)
  • 1 1/4 cups coarsely grated Parmesan cheese
  • salt and fresh ground black pepper to taste


  1. Preheat oven to 400F/200C.
  2. Wash outside of spaghetti squash if it’s dirty, then cut squash in half lengthwise.
  3. Use a sharp pointed spoon to scrape out seeds and stringy gunk that’s around the seeds.
  4. Cut ends off squash if desired, then rub inside surface with olive oil and Italian Herb Seasoning (affiliate link).
  5. Put squash on baking sheet that you’ve sprayed with non-stick spray.
  6. Roast squash, starting to check after about 40 minutes and removing when squash is still firm but strings apart fairly easily into spaghetti-like strands.  (It took about 50 minutes for the large pieces of squash I had.)
  7. Let squash cool a few minutes if needed, then scrape out strands into a plastic bowl or baking pan and discard skins.
  8. Gently mix in pesto and the cup of coarsely grated Parmesan cheese, season with salt and fresh ground black pepper.
  9. Then pour squash/cheese mixture into a gratin dish and top with 1/4 cup more Parmesan cheese.
  10. Bake 20-30 minutes more, until mixture is slightly bubbling and cheese is melted and starting to brown. Serve hot.


Look for a spaghetti squash that's about 6 lbs.

Recipe created by Kalyn.

Nutrition Information:



Serving Size:


Amount Per Serving: Calories: 160Total Fat: 11gSaturated Fat: 4gTrans Fat: 0gUnsaturated Fat: 7gCholesterol: 15mgSodium: 407mgCarbohydrates: 10gFiber: 2gSugar: 3gProtein: 6g

Nutrition information is automatically calculated by the Recipe Plug-In I am using. I am not a nutritionist and cannot guarantee 100% accuracy, since many variables affect those calculations.

If you make this recipe I'd love to hear how it turns out. Leave a star rating or share on social media with the hashtag #KALYNSKITCHEN, thanks!

Twice-Baked Spaghetti Squash with Pesto and Parmesan

Low-Carb Diet / Low-Glycemic Diet / South Beach Diet Suggestions:
Twice-Baked Spaghetti Squash with Pesto is a perfect side dish for low-carb eating plans. I would eat it for any phase of the original South Beach Diet, but it might be a bit high in fat if you’re following the letter of the law for South Beach.

Find More Recipes Like This One:
Use Side Dishes for more recipes like this one. Use the Diet Type Index to find recipes suitable for a specific eating plan. You might also like to Follow Kalyn’s Kitchen on Pinterest to see all the good recipes I’m sharing there.

Historical Notes for this Recipe:
This recipe was first posted in 2009, and it’s been really popular on the site. It was last updated with more information in 2021.

Pinterest image of Twice-Baked Spaghetti Squash with Pesto

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    78 Comments on “Twice-Baked Spaghetti Squash with Pesto”

  1. This was delicious! I modified by using Trader Joe’s Onion Salt seasoning instead of Italian herbs since I’m not a fan of oregano & thyme; plus I stirred in 2 wedges of Garlic & Herb Laughing Cow cheese. I also baked the squash for longer the first round to make sure it was super tender. I would totally make this for others as a low-cal but indulgent side!

  2. Omg , this was AMAZING. And easy to make. Trust me, I’m a terrible cook!  This is going in the permanent rotation. 

  3. Actually, true parmesano reggiano is not vegetarian because it contains calf rennet. More here: https://www.bustle.com/p/parmesan-cheese-isnt-vegetarian-technically-neither-are-a-bunch-of-other-cheeses-61022

    As a self-described food writer, I think it behooves you to know a bit more about food before you shut down commenters who are actually correct. Or just run a quick Google search! 🙂