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Pesto Spaghetti Squash

This Pesto Spaghetti Squash makes for a deliciously simple low carb meal. Roasted spaghetti squash is tossed with tender chicken and a homemade pesto sauce and baked to cheesy perfection. Yum!

spaghetti squash pasta

The first time I cooked spaghetti squash, it was with a mix of curiosity and skepticism. How could a squash, even one as uniquely textured as spaghetti squash, stand in for my beloved pasta?

But by the time that first cheesy bite hit my taste buds, I was converted. Spaghetti squash isn't just a substitute for pasta- it's a dish that can proudly stand on its own. A healthier, lighter, yet equally comforting alternative.

spaghetti squash pasta

This Pesto Spaghetti Squash is…

  • Totally Delicious: A fresh, keto friendly take on pasta night that will surprise and delight your taste buds.
  • Comfort Food, Redefined: All the warmth and comfort of your favorite pasta dish, but with a lighter, low-carb twist.
  • Packed with Fresh Flavors: The homemade pesto, with its bright basil and rich pine nuts, brings a depth of flavor that makes this dish unforgettable.
  • Cheesy Perfection: The golden, bubbly cheese topping adds a layer of indulgence that makes every bite a treat.
spaghetti squash pasta

Key Ingredients & Substitutions

Spaghetti Squash

The star of the show, offering a unique texture and sweetness. Choose a spaghetti squash that feels firm to the touch, without any cracks or soft spots.

Homemade Pesto

Fresh and vibrant, it's worth the effort to make it fresh. But in a pinch, a high-quality store-bought pesto can work too.


Adds a protein boost, making the dish more filling. 


I used a combination of Mozzarella and Parmesan cheese for the perfect melt. Feel free to experiment with different cheeses like Gruyère or fontina for a tasty twist.

spaghetti squash pasta

Helpful Tips for Pesto Spaghetti Squash

Roasting is Key

Don't rush the roasting process of the squash. It's essential for developing the flavor and stringy texture.

Customize Your Pesto

Taste as you go and adjust the garlic, cheese, or salt to suit your preferences. Pesto is forgiving and flexible, so get creative.

Storing Leftovers

Store leftover spaghetti squash in the refrigerator in a covered container for 3-4 days.

Serving Ideas

For a full Italian themed feast, serve your pesto spaghetti squash with a fresh green salad with low carb Italian dressing and my almost-zero-carb garlic bread.

spaghetti squash pasta


Make it Vegetarian: Skip the chicken or substitute with chickpeas or white beans, for a meatless version.

Make it Nut-Free: Swap out pine nuts for sunflower seeds or omit them altogether for a nut-free version.

Add More Veggies: Mix in roasted cherry tomatoes, sautéed mushrooms, or spinach to add more vegetables to the dish. Or check out this spaghetti squash with burrata and roasted tomatoes!

Fun Pesto Variations: Try it with a homemade spinach pesto or lemon pesto for a flavor twist.

spaghetti squash pasta

More Low Carb Recipes to Try

If you love this Pesto Spaghetti Squash, be sure to check out these other tasty ideas: 

spaghetti squash pasta

Pesto Spaghetti Squash

Yield: 4 servings
Prep Time: 20 minutes
Cook Time: 1 hour 10 minutes
Total Time: 1 hour 30 minutes

This low carb Pesto Spaghetti Squash is made with roasted spaghetti squash tossed with tender chicken and a homemade pesto sauce and baked to cheesy perfection.


  • 1 large spaghetti squash
  • 1 tablespoon olive oil
  • Salt and pepper to taste
  • pesto sauce
  • 1 cup pre-cooked shredded or diced chicken
  • ½ cup shredded mozzarella
  • ½ cup shredded parmesan cheese

Pesto Sauce

  • ¼ cup pine nuts
  • 2 cups basil leaves
  • ¼ cup shredded parmesan cheese
  • 2 cloves garlic
  • ½ teaspoon salt
  • ¼ teaspoon red pepper flakes
  • ¼ cup olive oil


  1. Preheat the oven to 400F, line a baking sheet with foil and set aside
  2. Slice the spaghetti squash lengthwise down the middle, then massage the oil into the cut side of the squash, then sprinkle with salt and pepper.spaghetti squash pasta
  3. Place the squash cut side down on the baking sheet and roast in the preheated oven for 45-50 minutes, or until the squash is soft enough to be pierced through with a butterknife. Remove from the oven and allow to cool until squash can comfortably be handled.spaghetti squash pasta
  4. Meanwhile, prepare the pesto by placing toasting the pine nuts in a medium pan over medium heat for 5 minutes. Remove from heat and allow to cool for 10 minutes.spaghetti squash pasta
  5. Add the pine nuts, basil leaves, parmesan cheese, garlic cloves, salt and red pepper flakes to a high speed food processor and pulse until everything is roughly chopped.spaghetti squash pasta
  6. Set the food processor to high, then slowly add the oil in a steady stream until the mixture is blended.spaghetti squash pasta
  7. Once the squash is cool enough to handle, use a fork to scrape the flesh spaghetti squash pasta
  8. And transfer into a large bowl.spaghetti squash pasta
  9. Add the chicken and desired amount of pesto with the spaghetti squash and stir to combinespaghetti squash pasta
  10. Transfer to a small baking dish and top with mozzarella and parmesan. spaghetti squash pasta
  11. Return to the oven and bake for an additional 10-20 minutes, or until the cheese is bubblingspaghetti squash pasta
  12. Allow to cool slightly before servingspaghetti squash pasta
spaghetti squash pasta
spaghetti squash pasta
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