Twice-baked Pesto Spaghetti Squash topped with Parmesan is a delicious idea that’s perfect for a low-carb meatless meal or a cheesy side dish. And I think the combination of spaghetti squash, pesto, and Parmesan cheese is a perfect way to make mild spaghetti squash into a dish that’s bursting with flavor!

PIN Pesto Spaghetti Squash to try it later!

spaghetti squash baked with pesto in serving dish with plates and forks

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 spaghetti squash as 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’m featuring this recipe as my Friday Favorites pick this week to remind you about this ultra popular Pesto Spaghetti Squash that’s baked and shredded apart, mixed with pesto and Parmesan, and baked again in a casserole dish. Yum! 

What ingredients do you need for this recipe?

(This is only a list of ingredients; please scroll down for complete printable recipe. Or if you use the JUMP TO RECIPE link at the top of the page, it will take you directly to the complete 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

What pesto did I use for the Pesto Spaghetti Squash?

Spaghetti squash shows up in the garden about the time many people start making pesto with their abundant summer basil, and I’ve been making Basil Pesto with Lemon and storing it in the freezer for years and years. That’s the pesto I’d always use for this recipe if I had some, but if you don’t have any homemade pesto you can certainly use my favorite pesto in a jar for this recipe.

Want more spaghetti squash recipes?

Check out Spaghetti Squash Recipes for more ways to use this favorite fall vegetable. This post was included in a round-up of Cheesy Low-Carb Spaghetti Squash Recipes.

Do you love Pesto?

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

Pesto Spaghetti Squash process shots collage

How to make Pesto Spaghetti Squash:

(This is only a summary of the steps for the recipe; please scroll down for complete printable recipe. Or if you use the JUMP TO RECIPE link at the top of the page, it will take you directly to the complete 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.

spaghetti squash baked with pesto shown in baking dish

Make It A Low-Carb Meal:

Pesto Spaghetti Squash would taste great served with Grilled Boneless Pork Chops, Chicken Souvlaki, Grilled Cuban Flank Steak, Baked Parmesan Crusted Chicken, or Air Fryer Chicken Drumsticks for a low-carb meal.

More Meatless Ideas for Spaghetti Squash:

Weekend Food Prep:

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

Twice-Baked Spaghetti Squash with Pesto in baking sheet with plates and forks
Yield: 8 servings

Pesto Spaghetti Squash

Prep Time 15 minutes
Cook Time 1 hour 20 minutes
Total Time 1 hour 35 minutes

Spaghetti squash is baked and the mixed with pesto and Parmesan and baked again in this delicious recipe for Pesto Spaghetti Squash!


  • 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.

Did you make this recipe?

Did you make this recipe? Please leave a star rating (under the PRINT button in the recipe) or share a photo of your results on Instagram! THANKS!

square image of Pesto Spaghetti Squash on baking dish

Low-Carb Diet / Low-Glycemic Diet / South Beach Diet Suggestions:
Pesto Spaghetti Squash is a perfect side dish for low-carb or Keto 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, on Facebook, on Instagram, on TikTok, or on YouTube 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 ever since then. It was last updated with more information in 2023.

Pinterest image of Pesto Spaghetti Squash

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