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Kalyn's Kitchen

Twice-Baked Spaghetti Squash with Pesto and Parmesan

Twice-Baked Spaghetti Squash with Pesto and Parmesan is a delicious side dish that’s low-carb, Keto, low-glycemic, meatless and gluten-free. Check out Spaghetti Squash Recipes for more ways to use this favorite fall vegetable!

Click to PIN Twice-Baked Spaghetti Squash with Pesto and Parmesan!

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

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 spaghetti squash as a substitute for pasta, I love to eat it as a side dish or as the base of a bowl meal. And fall is when the best spaghetti squash shows up in the stores or Farmers market, so I thought it was a good time to remind you about this ultra popular Twice-Baked Spaghetti Squash with Pesto and Parmesan. I recently noticed on Pinterest that one of my pins of this recipe has been re-pinned more than 50K times, so it seems like a lot of people like this recipe!

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.

And this delicious spaghetti squash casserole doesn’t need any meat, making this a perfect Meatless Monday dish for this time of year. And check out My Favorite Low-Carb and Keto Recipes with Pesto for more tasty ideas for using basil pesto!

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

Cut spaghetti squash in half lengthwise and use a sharp spoon to scrape out the seeds and stringy gunk that’s around the seeds. Rub the cut sides with some olive oil and sprinkle with a little Italian Herb blend. Roast the squash at 400F/200C until the squash pulls apart easily with a fork like this.

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!) Here’s how it looked when the squash, pesto, and Parmesan was evenly mixed.

I transferred it to this baking dish which is about 12 inches by 8 inches. Sprinkle with grated Parmesan. Bake 20-30 minutes more, or until it’s bubbling and starting to brown.

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

Serve hot, with additional Parmesan to add at the table if desired.

More Meatless Ways to Cook Spaghetti Squash:

Mediterranean Spaghetti Squash Sauteed 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
Vegan Spaghetti Squash and Black Bean Mexican Bowl ~ Kalyn’s Kitchen

Weekend Food Prep:

This recipe has been added to a new 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 and Parmesan

Spaghetti squash is delicious with pesto and Parmesan!


  • 1 large spaghetti squash (6-8 lbs.)
  • 1-2 T olive oil (depending on how big your squash is)
  • 1-2 tsp. Italian Herb Blend (or use other seasoning of your choice)
  • 3 T basil pesto (more or less to taste)
  • 1 cup + 1/4 cup 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. Use a sharp pointed spoon to scrape out seeds and stringy gunk that’s around the seeds.
  3. Cut ends off squash if desired, then rub inside surface with a small amount of olive oil and Italian Herb Blend. Put squash on baking sheet that you’ve sprayed with non-stick spray.
  4. 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.)
  5. Let squash cool a few minutes if needed, then scrape out strands into a plastic bowl or baking pan and discard skins.
  6. Gently mix in pesto and the cup of coarsely grated Parmesan cheese, season with salt and fresh ground black pepper, then pour squash/cheese mixture into a gratin dish and top with 1/4 cup more Parmesan cheese.
  7. Bake 20-30 minutes more, until mixture is slightly bubbling and cheese is melted and starting to brown. Serve hot.


Recipe created by Kalyn.

All images and text ©

Low-Carb Diet / Low-Glycemic Diet / South Beach Diet Suggestions:
Twice-Baked Spaghetti Squash with Pesto and Parmesan is a perfect side dish for any phase of the South Beach Diet and other low-carb eating plans.

Find More Recipes Like This One:
Use the Recipes by Diet Type photo index pages to find more 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.

Nutritional Information?
If you want nutritional information for a recipe, I recommend entering the recipe into this nutrition analyzer, which will calculate it for you. Or if you’re a member of Yummly, you can use the Yum button on my site to save the recipe and see the nutritional information there.


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76 comments on “Twice-Baked Spaghetti Squash with Pesto and Parmesan”

  1. Pingback: 10 More Veggie-Packed Keto Vegetarian Recipes to Try - Hello Veggie

  2. This is delicious!  It was my first time to cook a spaghetti squash.  My in-laws seem to hate all vegetables though so I have lots leftover from this side dish I included in our holiday dinner.  I wanted to add more cheese and spices, when I ate it for lunch today.  We also have too much of the cream cheese and herbs left over from appetizers.  I added some to the hot squash and that was yummy too!

  3. My oven is going to be pretty full this Christmas Eve. I want to make this for Christmas Eve dinner and was wondering if  twice baked spaghetti squash with pesto and Parmesan would work in a crockpot?

    • I haven’t done it so I can only say “maybe”. My concern is that the slow cooker produces more liquid and I like the way the oven dries out the spaghetti squash when it roasts. Sorry I can’t be more definite; would love to hear how it works if you try it!

  4. Pingback: Dinner Shortcut - Quick Spaghetti Squash - Made Over Meal

  5. Pingback: Friday Faves | foodiecrush

  6. Do you bake the squash cut side up or cut side down on baking pan ?

  7. Parmesan is not vegetarian…

  8. Pingback: Spaghetti Squash with Sausage and Mushroom Bolognese

  9. What is the carb amount in the Twice Baked Spaghetti Squash? It doesn’t state. Thank you! 🙂

    • I give two links after the recipe itself (where it says “Nutritional Information”) for suggestion of how to get that information. I’m not able to provide nutritional information for the recipes for several reason, including the additional time it takes, the difficulty in doing it accurately, and the sheer number of recipes on my site. That’s all I can do at this time. Thanks for understanding.

  10. I'm on the Keto diet and made this Friday when my vegetarian friend came to dinner. We both loved it. And it was even good as a left over. Thanks so much for a recipe I'm sure I'll make many times again!

  11. I do a version of this but add ground turkey, onions, mushroom and garlic. Everyone who tastes it, loves it! I use the Knorr pesto mix as my seasoning, but only use the olive oil that I sautéed the onions, etc. in. I add some water to create the sauce. Delicious, low carb, filling, and satisfying. Roast the squash first, sauté turkey meet, remove from pan, and sauté onions, etc with a little olive oil. Cook about 3/4 of the way through, add Knorr pesto packet, spaghetti squash, cooked ground turkey, and a little water, cover and simmer for 10 minutes. I sprinkle parmesan cheese on each serving as I eat it because it lasts a few days for me. Enjoy!

  12. I was wondering if this would still have the crunchy look w/o cheese? I'm starting Whole 30 so no cheese plus I don't eat cheese. April

  13. I would like to make this for dinner tonight (and likely the next few nights since I'll be the only one eating it). Does anyone think this might work with mozzarella? I'm not a huge fan of permesan since there is already some in the Classico pesto I use?

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