This Chicken Pesto Spaghetti Squash (Paleo, Keto, Whole30) is comfort-food simplicity with a bright, fresh twist. Roasted spaghetti squash provides a light, noodle-like base while juicy, seasoned chicken thighs and a vibrant, nut-free pesto bring richness and herb-driven flavor. It’s an excellent weeknight dinner that’s naturally grain-free and adaptable for Keto, Paleo, and Whole30 preferences. The texture contrast between tender squash strands and the creamy, slightly oily pesto makes every forkful satisfying without feeling heavy.

Why you’ll love this recipe

Low-carb and naturally gluten-free thanks to spaghetti squash replacing pasta.
Uses pantry-friendly fats like avocado oil, which keeps the recipe neutral and mild.
Quick to assemble: while the squash roasts, you can season and cook the chicken and blitz the pesto.
Easy to customize: omit the optional parmesan for Whole30 compliance or keep it for a richer flavor.

Ingredients

Makes about 4 servings

1 large roasted spaghetti squash
2 Tbsp avocado oil
1 pinch sea salt
1 Tbsp avocado oil
1 1/2 lbs boneless chicken thighs, chopped
1 tsp paprika
1 tsp garlic powder
1/4 tsp sea salt to taste
2 cup fresh basil leaves
2/3 cup pumpkin seeds (see note)
2/3 cup avocado oil
1 large clove garlic
1 cup parmesan (optional, omit for whole30)

Equipment

Baking sheet
Knife and cutting board
Large skillet
Food processor or high-speed blender
Mixing bowls
Tongs or fork for shredding squash

Prep and timing

Total time: about 55–65 minutes depending on your oven and whether you roast the squash whole or halved. Most of the work happens simultaneously: while the squash roasts, you’ll prepare the pesto and cook the chicken.

Step-by-step Instructions

Follow these clear, sequential steps to prepare the Chicken Pesto Spaghetti Squash (Paleo, Keto, Whole30). The directions keep the same order as the source recipe ingredients and match each ingredient name and amount exactly.

Roast the spaghetti squash: Preheat your oven to 400°F (200°C). If your squash is very large, you can slice it in half lengthwise; otherwise roast whole. Carefully cut the spaghetti squash in half lengthwise, scoop out the seeds, and brush the cut sides with 2 Tbsp avocado oil. Sprinkle with 1 pinch sea salt. Place the squash halves cut-side down on a baking sheet lined with parchment or lightly oiled. Roast until the flesh is tender and easily strands with a fork, about 35–45 minutes depending on size. If you roasted the squash whole, roast until soft, then halve and shred as below.
Shred the roasted squash: Remove the roasted squash from the oven and let it cool 5–10 minutes until it’s safe to handle. Use a fork to scrape the flesh into long strands into a large bowl. Set aside while you prepare the chicken and pesto.
Season the chicken: In a medium bowl, combine the chopped 1 1/2 lbs boneless chicken thighs with 1 tsp paprika, 1 tsp garlic powder, and 1/4 tsp sea salt (use a little more or less to taste). Toss until the chicken pieces are evenly coated with the spices.
Cook the chicken: Heat 1 Tbsp avocado oil in a large skillet over medium-high heat. Add the seasoned chicken thigh pieces in a single layer, taking care not to overcrowd the pan. Cook, stirring and turning occasionally, until the chicken is cooked through and browned at the edges, about 6–8 minutes depending on piece size. Once cooked, remove from heat and set aside. Keep warm.
Make the pesto: While the chicken cooks, assemble the pesto. In a food processor or high-speed blender place 2 cup fresh basil leaves, 2/3 cup pumpkin seeds, 1 large clove garlic, and 2/3 cup avocado oil. If you are including cheese, add 1 cup parmesan now; if you are preparing a Whole30 version, omit the parmesan. Pulse or blend until the mixture reaches a smooth, slightly coarse emulsion—scrape down the sides as needed and blend again to combine. Taste and adjust the seasoning; add a pinch of sea salt if needed.
Toss squash with pesto: Add roughly half of the pesto to the bowl of shredded spaghetti squash and toss gently to coat the strands. Add more pesto as desired until the squash is evenly flavored but not overly oily. You want bright basil flavor throughout without overwhelming the delicate squash texture.
Combine chicken and squash: Gently fold the cooked chicken pieces into the pesto-coated spaghetti squash. Taste and add the remaining 1/4 tsp sea salt to taste if necessary. Reheat briefly in the skillet over low heat if you prefer the dish warm, stirring for 1–2 minutes just to bring everything together.
Serve: Divide the Chicken Pesto Spaghetti Squash (Paleo, Keto, Whole30) among plates or bowls and finish each serving with a swirl of remaining pesto if you reserved any. For non-Whole30 eaters, grate a little extra parmesan on top if desired. Serve immediately.

Notes and tips

Pumpkin seed swap: The recipe calls for 2/3 cup pumpkin seeds. These provide a nut-free pesto base that is suitable for those avoiding tree nuts. If you prefer, you can substitute sunflower seeds or blanched almonds unless you need a nut-free option—keep the same amount.
Parmesan: The 1 cup parmesan is optional. Omit it entirely for Whole30 compliance or keep it for richer flavor and a creamier pesto texture. If you want a dairy-free but not Whole30 constraint alternative, nutritional yeast can add a cheesy note (use to taste).
Roasting method: Roasting the squash cut-side down concentrates moisture and caramelizes the edges. If your oven is busy, you can microwave the halved squash face-down for 10–12 minutes to soften it before finishing in the oven for 8–10 minutes to develop a roasted flavor.
Chicken cuts: The recipe specifies boneless chicken thighs because they stay juicy and flavorful when pan-seared. If you only have breasts, use them and slightly reduce the cooking time so they don’t dry out.
Pesto texture: If your pesto is too thick, add a tablespoon of water or more avocado oil and blend again until you reach the desired consistency. If it’s too thin, add a few more pumpkin seeds or a small handful of basil to thicken.
Storage: Store leftovers in an airtight container in the refrigerator for up to 3 days. Reheat gently in a skillet over low heat to avoid drying the chicken or mushy squash.

Variations

Protein swap: Substitute cooked shrimp or diced turkey for the chicken if you prefer. Keep the same seasoning amounts and adjust cook time for the protein you choose.
Veggie boost: Toss in halved cherry tomatoes or sautéed mushrooms when combining the chicken and squash for added texture and volume.
Spicy pesto: Add a pinch of crushed red pepper flakes to the pesto or a small finely chopped jalapeño to brighten and add heat.

Common questions

Can I make the pesto ahead? Yes. The pesto can be made up to 2 days in advance and stored in the refrigerator in a sealed container. Press a layer of plastic wrap directly onto the surface of the pesto to minimize browning.

How do I know when the spaghetti squash is done? The squash is ready when a fork easily pulls out long strands and the flesh feels tender. If the strands resist or the flesh feels firm, roast a bit longer and check again every 5–7 minutes.

Is spaghetti squash filling enough to replace pasta? For many people, yes. The strands mimic the texture of thin pasta and when tossed with pesto and chicken they create a satisfying, lower-carb alternative. If you want more volume, add extra vegetables or a side salad.

Final thoughts

This Chicken Pesto Spaghetti Squash (Paleo, Keto, Whole30) is a lovely balance of roasted, herbaceous, and savory flavors. It’s approachable enough for a weekday dinner and presentable enough for company. Using boneless chicken thighs ensures tenderness, while the pumpkin-seed-based pesto keeps the sauce grain- and nut-free. Whether you’re new to spaghetti squash or looking for a fresh way to enjoy chicken and pesto, this dish delivers vivid basil flavor with a satisfying contrast of textures.

Enjoy this recipe as a standalone main or pair it with a crisp green salad and a squeeze of lemon for brightness. It’s a simple way to get dinner on the table with fresh flavors that feel both nourishing and indulgent.