
Chicken pesto spaghetti squash with juicy chicken thighs and fresh homemade basil pesto is one of those meals that feels totally special but comes together in a surprisingly simple way. When I want something that is vibrant hearty and fits just about every healthy eating plan this is it. Perfect for busy weeknights or meal prep days when you need a big pan of something satisfying.
I first tossed this together after a friend dropped off garden basil and it was the first time my pasta-loving husband asked for seconds on spaghetti squash.
Ingredients
- Spaghetti squash: Roasted to create long tender strands that absorb flavor Look for one that feels heavy for its size and has a firm unblemished skin
- Avocado oil: Adds creaminess and good fats Choose cold pressed for best results
- Sea salt: Brings out the sweetness in both the squash and chicken Go for a fine sea salt so it incorporates easily
- Chicken thighs: Boneless and chopped so every bite is juicy and flavorful Choose organic or pasture-raised for unbeatable taste
- Paprika: Warmth and gentle color Spanish or Hungarian paprika both work beautifully
- Garlic powder: Seasoning for building savory depth Select pure garlic powder no blends
- Fresh basil leaves: The star of pesto Use bright green vibrant leaves for ultimate freshness
- Pumpkin seeds: A nut free twist on pesto that gives body and crunch Raw unsalted pepitas are best
- Avocado oil: Makes the pesto extra velvety Another healthy and neutral choice
- Garlic: Adds zing to the pesto Use a fresh large clove for that punch
- Parmesan cheese: Optional skip this for Whole30 and use the best quality block you can find for grating
Tips for selecting Choose ingredients as fresh as possible and when making pesto always wash and dry basil thoroughly for best sauce texture.
Step-by-Step Instructions
- Roast the Spaghetti Squash:
- Bake your squash whole or halved at 400F until you can easily pierce it with a fork usually 40 to 45 minutes Depending on squash size you may need a bit longer Let it cool enough so you can handle it safely then use a fork to shred the insides into lovely noodle-like strands
- Make the Homemade Pesto:
- Add fresh basil pumpkin seeds garlic and parmesan if using to a food processor and pulse a few times to rough chop With the machine running slowly pour in avocado oil until the pesto is thick but spoonable Scrape down the sides and pulse again until smooth taste and adjust salt if needed
- Brown the Chicken:
- Heat a heavy skillet over medium-high then add avocado oil and chopped chicken Sprinkle with paprika garlic powder and sea salt Spread the chicken in a single layer and let it cook without stirring for three minutes so it gets nice and golden Flip or stir and brown the other side the same way Cover and cook through two to five minutes more until the juices run clear
- Combine and Finish:
- Transfer the shredded squash to a large mixing bowl Toss it with pesto until every strand is coated Add the chicken along with all pan juices and gently fold together Taste and season with sea salt as needed so the flavors really pop
- Serve and Enjoy:
- Spoon your chicken pesto spaghetti squash into bowls and make sure to get a little of everything in each serving If you opted for parmesan sprinkle a touch more on top

Storage Tips
Keep leftovers in a sealed container in the refrigerator for up to four days The squash absorbs flavor overnight so it tastes even better the next day You can reheat gently in a skillet or microwave but be careful not to overcook the chicken so it stays juicy
Ingredient Substitutions
Pine nuts walnuts almonds or pecans all work in place of pumpkin seeds If you do not have chicken thighs you can use chicken breast just watch the cooking time so it does not dry out For dairy free or Whole30 skip parmesan and try adding a tablespoon of nutritional yeast to the pesto for cheesy flavor
Serving Suggestions
Serve warm in bowls with extra fresh basil on top For added veggie power toss in baby spinach or halved cherry tomatoes right before serving This recipe is satisfying enough for dinner but makes a perfect lunchbox dish when cold

Cultural and Historical Context
Spaghetti squash is often called nature’s pasta and has been a creative substitute for noodles in Italian-inspired dishes for years Swapping nuts for seeds in pesto is an old kitchen trick that makes this dish accessible for those with nut allergies and adds its own unique twist
Frequently Asked Questions
- → Can I use chicken breast instead of thighs?
Yes, chicken breast works well in this dish, though chicken thighs add extra moisture and flavor.
- → What can I substitute for pumpkin seeds in the pesto?
Pine nuts, almonds, walnuts, or pecans are great alternatives for pumpkin seeds in the pesto.
- → Is this meal suitable for Whole30?
Yes. Omit the parmesan cheese in the pesto to ensure the meal remains Whole30 compliant.
- → How do I achieve the best spaghetti squash texture?
Roast the squash cut-side down until tender, then use a fork to scrape out the spaghetti-like strands.
- → Can I make the pesto in advance?
Absolutely! Store homemade pesto in the fridge for up to a week, or freeze for longer storage.
- → Is this meal freezer-friendly?
While you can freeze it, the texture of spaghetti squash may become a bit softer after thawing.