Pesto Chicken and Spaghetti Squash Bake (Low Carb, Gluten Free)

Low Carb, Gluten Free, Family Friendly

Prep Time 10 minutes
Cook Time 15 minutes
Total Time 25 minutes


  • 5 cups cooked spaghetti squash about 1 small-medium squash
  • 2 1/2 cups chicken breasts about 1 lb
  • 1 cup pesto
  • salt and pepper to taste
  • 1/2 tsp garlic powder
  • 1/2 tsp onion powder
  • 8 oz grated mozzarella cheese about 1 1/2 cups
  • 3 tbsp parmesan cheese
  • 2-3 medium tomatoes


  • 1 1/2 cups packed basil leaves
  • 1 clove garlic blanched
  • 1/4 cup pine nuts
  • 1/4 cup sunflower seeds
  • 3 tbsp lemon juice
  • 1/4 tsp salt
  • 1/4 tsp pepper
  • 1/4 cup parmesan reggiano cheese grated
  • 1/2 cup olive oil


Prepare Squash

  1. Cook the squash your preferred way - I cook it in the Instant Pot or roast it in the oven. Scoop the seeds out and scrape the squash out with forks, breaking it up a bit and fluffing it up as you remove it. 

Make the Pesto

  1. Add all the ingredients except the oil to your high speed blender or food processor. Pulse a few times until combined. 

  2. Add the oil and blend together on low until fully combined. Add additional oil if necessary until it reaches your desired consistency, 1 teaspoon at a time. 

Prepare the Dish

  1. Preheat your oven to 400 degrees. Chop or shred the chicken into bite-sized pieces. Slice the tomatoes into 1/2 inch slices and set them aside.

  2. In a large bowl, toss the chicken, spaghetti squash, pesto and seasonings together. 

  3. Pour the mixture into to a 10-inch casserole dish and gently press the mixture down. 

  4. Sprinkle the mozzarella and parmesan cheese over the spaghetti squash mixture, then lay the tomato slices on top. 

  5. Bake for 12-15 minutes, until the cheese is melted and it's heated through. You can finish it under the broiler for a minute or two to brown the cheese a bit, if you'd like!