Chicken Pesto Spaghetti Squash (Paleo, Keto, Whole30)

This Chicken Pesto Spaghetti Squash (Paleo, Keto, Whole30) is exactly the kind of weeknight dinner I reach for when I want something bright, comforting, and low-carb without sacrificing flavor. Tender, seasoned chicken thigh pieces mingle with nutty, herb-forward pesto that clings to strands of roasted spaghetti squash. It’s a one-pan feeling even when parts are finished separately, and it comes together quickly once the squash is roasted. The result is cozy and fresh at once: creamy, herbaceous, and satisfyingly hearty.

Why you’ll love this recipe

• Low-carb and nutrient-dense: spaghetti squash replaces pasta with a lighter, vitamin-rich base.
• Big flavor: a pumpkin seed-based pesto brings rich, toasty notes and vibrant basil aroma.
• Simple protein: boneless chicken thighs stay juicy and are seasoned with a comforting spice blend.
• Meal-prep friendly: make extra pesto or chicken to toss with greens or roasted vegetables later in the week.

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 cups 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 and parchment or silicone mat
• Large skillet
• Food processor or high-powered blender
• Mixing bowls and utensils
• Fork to shred the squash into strands

Prep ahead

Roast the spaghetti squash up to 2 days ahead and store it in the fridge. The pesto keeps for 3–4 days in an airtight container. Cooked chicken will keep 3–4 days refrigerated, so this recipe is very friendly to make-ahead strategies.

Step-by-step instructions

The following steps rewrite the original directions into clearer, sequential instructions. Amounts and ingredient names match the ingredient list above.

1. Roast the spaghetti squash. Preheat your oven to 400°F (205°C). Slice the large spaghetti squash in half lengthwise, scoop out the seeds, and place the halves cut-side down on a parchment-lined baking sheet. Brush or rub the cut surfaces with 2 Tbsp avocado oil and sprinkle with a pinch of sea salt. Roast until the flesh is tender and the strands pull away easily with a fork, about 35–50 minutes depending on the size. Once roasted, let the squash cool slightly, then use a fork to scrape out the strands into a large bowl. Set aside.
2. Season and cook the chicken thighs. While the squash roasts, prepare the chicken. Place the chopped boneless chicken thighs in a bowl and drizzle with 1 Tbsp avocado oil. Sprinkle on 1 tsp paprika, 1 tsp garlic powder, and 1/4 tsp sea salt (adjust to taste). Toss the chicken so it is evenly coated with the spices and oil.
3. Sear the chicken. Heat a large skillet over medium-high heat. When the pan is hot, add the seasoned chicken in a single layer. Cook, stirring occasionally, until the chicken pieces are cooked through and lightly browned on the outside, about 6–8 minutes depending on the size of the pieces. Transfer the cooked chicken to a plate and keep warm.
4. Make the pumpkin seed pesto. In a food processor or high-powered blender, combine 2 cups fresh basil leaves, 2/3 cup pumpkin seeds, 2/3 cup avocado oil, and 1 large clove garlic. If you are including cheese, add 1 cup parmesan at this point; otherwise omit for Whole30. Pulse the mixture until smooth but still slightly textured, scraping down the sides as needed. Taste and add a pinch of sea salt if needed. The pesto should be bright and aromatic, with a slightly nutty character from the pumpkin seeds.
5. Toss spaghetti squash with pesto and chicken. Add the roasted spaghetti squash strands back to the large bowl (or use the same skillet on low heat). Spoon in the pesto and toss gently to coat the strands evenly. Add the cooked chicken and fold everything together so the chicken and squash are well distributed and glossy with pesto.
6. Adjust seasoning and serve. Taste and adjust for seasoning, adding more salt or a drizzle of avocado oil if you want extra richness. Divide the Chicken Pesto Spaghetti Squash (Paleo, Keto, Whole30) among bowls and garnish with extra basil leaves or a sprinkle of pumpkin seeds for texture. If using parmesan, a little more on top is lovely.

Taste and texture notes

The strands of spaghetti squash are mild and slightly sweet, which lets the pesto shine. Using pumpkin seeds instead of pine nuts gives the pesto a toasty backbone and keeps the recipe compliant with paleo and Whole30 where pine nuts may sometimes be avoided; it also keeps cost down. Avocado oil is the neutral, high-heat oil that plays well with the chicken and pesto while keeping the total fat profile aligned with keto goals. Boneless chicken thighs stay juicy and have more flavor than breast meat when pan-seared, which complements the herb-forward pesto.

Substitutions and variations

• Protein swap: If you prefer white meat, swap the chicken thighs for 1 1/2 lbs boneless chicken breast pieces. Watch cooking time closely to avoid drying them out.
• Nut-free pesto: This recipe already uses pumpkin seeds; you can also use toasted sunflower seeds if you prefer.
• Dairy-free: Omit the parmesan to keep it fully compliant with Whole30 and dairy-free diets. The pesto is still rich thanks to the oil and pumpkin seeds.
• Herb boost: Stir in a handful of chopped parsley or arugula for an extra green note.

Serving suggestions

• Serve warm as a main dish with a side salad dressed in lemon and olive oil.
• Turn leftovers into a warm lunch bowl with roasted vegetables or leafy greens.
• For an extra-special plate, spoon the squash and chicken into roasted portobello mushrooms for a rustic presentation.

Make-ahead and storage

Store any leftovers in an airtight container in the refrigerator for up to 3–4 days. Reheat gently in a skillet over low heat with a splash of water or extra avocado oil to loosen the pesto. The pesto itself will keep separately in the fridge for 3–4 days and can be frozen for longer storage. Roasted spaghetti squash can be reheated easily or eaten cold in salads.

Notes

• Pumpkin seed note: Pumpkin seeds add great texture and flavor. If you prefer a smoother pesto, toast the seeds lightly in a dry skillet until fragrant before blending.
• Roasting time will vary by squash size. Start checking for doneness at 35 minutes; the flesh should be tender and easily shredded with a fork.

Final thoughts

This Chicken Pesto Spaghetti Squash (Paleo, Keto, Whole30) is a weeknight winner: quick to assemble, full of layers of flavor, and flexible enough to work for multiple dietary preferences. The pumpkin seed pesto is bright and bold, the chicken is seasoned simply but thoughtfully, and the roasted squash brings a lovely texture that makes this feel indulgent without being heavy. Keep an eye on the seasoning and adjust the pesto to your taste, and you’ll have a dependable meal that keeps well and shines as leftovers too.