Creamy Pesto Spaghetti Squash Bake with Chicken and Tomatoes

Cheesy Pesto Spaghetti Squash Bake
Grain Free Keto Friendly Kid Friendly Low Carb One Pan 

Nutrition: 518 Calories | 15.9g Net Carbs | 28.4g Protein | 37.2g Total Fat

This easy pesto spaghetti squash bake with ground chicken, a creamy cheese layer, fresh tomatoes and melted mozzarella is a tasty make-ahead meal.

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If you’re looking for a fun and flavorful make-ahead meal, this pesto spaghetti squash bake is it. With layers of spaghetti squash, creamy cheese filling, and a chicken pesto sauce, it’s kind of like a fancy lasagna, without the pasta. This makes it the ideal make-ahead meal. And, it’s the perfect dish to drop off to busy families too. Basically a twist on my spaghetti squash casserole with ground beef, this recipe comes together quickly. Then, you can keep it in the refrigerator until you’re ready to bake it.

Bake the Spaghetti Squash and Prep Some Vegetables

This recipe requires one whole spaghetti squash cooked. Spaghetti squash is pretty simple to prepare. First, you need to cut the squash in half and clean out the inside. Then, you bake it until the squash is tender. If you’ve never made spaghetti squash before, I made a whole post about it. Check out my post for Easy Spaghetti Squash to get all the details. Once the spaghetti squash is cooking, dice up one medium onion for the pesto sauce layer. Also, thinly slice one medium tomato and save it for later.

Make the Chicken Pesto Sauce Layer on the Stove

Now that you’ve finished the quick prep work, it’s time to start making the tasty chicken pesto layer for your spaghetti squash bake. First, heat a pan on the stove over medium heat. Once the pan is ready, add your diced onion to the pan and about a tablespoon of pesto. Stir it all together, and sauté the onions until they are soft. Normally, I would sauté the onions with some olive oil. However, pesto is made with olive oil, so using it to sauté the onions is an easy swap with lots of flavor.

When the onions are soft and translucent, it’s time to add ground chicken to the pan. Break up the chicken, and stir it in with the onions. Continue stirring the mixture occasionally until the chicken in fully cooked. Finally, stir in your pesto sauce and mix it in with the meat mixture. Remove the pan from the heat, and set the chicken pesto sauce aside until it’s time to layer your dish.

If you can’t find any ground chicken at the grocery store, ground turkey it a great alternative. I’ve also used Italian sausage, which adds another layer of flavor.

Mix Up the Creamy Cheese Layer

While the chicken is cooking in the pan, it’s a good time to make the creamy cheese layer. So, add softened cream cheese and cottage cheese to a mixing bowl. Then, add in garlic powder and dried basil to season the cheeses. Mix it all together until you have a smooth, creamy mixture.

Gather Your Ingredients and Start Layering

When the cheese layer is ready, gather up the rest of your ingredients. You’ll need the cooked spaghetti squash and chicken pesto sauce. Also grab the sliced tomatoes from earlier and some shredded mozzarella cheese. Then, spray a 9″ by 13″ baking dish with non-stick spray.

After spraying your baking dish, add half of the spaghetti squash to the bottom. Spread it out into an even layer. Next, spread out half of the cheese mixture on top of the squash. Then, repeat with the remaining spaghetti squash and cheese filling.

Once you have two layers each of spaghetti squash and the cheese mixture, pour the chicken pesto sauce on top. Then, use the back of a spoon to smooth the sauce out evenly over the entire dish.

The last step is building your pesto spaghetti squash bake is to add shredded mozzarella and sliced tomatoes on top. Now, it’s ready to bake. Cook the pesto spaghetti squash bake in the oven at 350° until it’s bubbly around the edges. It’ll take about 30 minutes. Give the casserole time to rest after baking, about 10 minutes, then serve and enjoy.

Prepping Ahead of Time and Freezing

If your prepping your meal ahead of time, keep it in the refrigerator until you’re ready to cook. Give the dish time to come to room temperature or add another 10 minutes or so to the cook time to ensure it’s heated all the way through. This recipe makes a fun dish to deliver to families as part of a meal train too.

If you meal prepping and freezing dishes for later, this is a good recipe to add to your list. Just leave off the fresh tomatoes and freeze the rest. From frozen, it’ll take 55-65 minutes to bake. Add tomato slices halfway through the baking time or at the end, if you want that fresh flavor.

Other recipes to check out: Spaghetti Squash Casserole with Ground Beef, Spaghetti Squash Carbonara, and Chicken Margherita Keto Pizza Casserole with Cauliflower Rice.

Creamy Pesto Spaghetti Squash Bake with Chicken and Tomatoes

This easy pesto spaghetti squash bake with ground chicken, a creamy cheese layer, fresh tomatoes and melted mozzarella is a tasty make-ahead meal.

Total Time: 60 min
Prep Time: 30 min
Cook Time: 30 min


  • 1 Spaghetti Squash (about 3 pounds), cooked (Recipe Here)
  • 1 lb Ground Chicken
  • 8 oz Cream Cheese, softened
  • 2 Cups Cottage Cheese
  • 1 Cup Shredded Mozzarella Cheese
  • 1 Medium Onion
  • 1 Tomato, thinly sliced
  • 11 oz Pesto, divided
  • 1 tsp Dried Basil
  • 1 tsp Garlic Powder


  1. Prepare the spaghetti squash by roasting it in the oven. For more details, check out this post: Easy Spaghetti Squash Recipe.
  2. While the squash is cooking, dice the onion. Heat a pan on the stove over medium heat. When the pan is hot, add the diced onion and 1 tablespoon of pesto to the pan. Sauté the onion until it’s soft.
  3. When the onion is soft, add the ground chicken to the pan. Break up the meat and brown it, stirring occasionally. When the meat is fully cooked, stir in the remaining pesto sauce with the chicken and onions. Then, remove the pan from the heat and set aside.
  4. While the chicken is cooking, prepare the cream cheese layer. In a mixing bowl, combine the cream cheese, cottage cheese, garlic powder and dried basil. Mix everything together until it’s creamy and throughly combined. Set the cheese mixture aside.
  5. Spray a 9″ by 13″ baking dish with non-stick spray. Add half of the cooked spaghetti squash to the dish, and spread it out in an even layer. Next, layer half of the cheese mixture on top of the squash and smooth it out evenly. Repeat the process with the remaining squash and cheese mixture.
  6. Pour the pesto chicken sauce over the top of the layers in the baking dish making sure it covers all the cheese mixture. Top the pesto sauce with the shredded mozzarella. Lastly, layer the sliced tomatoes on top of the shredded cheese.
  7. Bake the spaghetti squash dish at 350° for about 30 minutes until it is bubbly around the edges. Let it rest for about 10 minutes before serving. If you refrigerate the dish before baking, add about 10 more minutes to the bake time. 


Yield: 8 servings, Serving Size: About 1.5 Cups

Amount Per Serving:  Calories: 518,  Total Fat: 37.2g, Saturated Fat: 9.7g,  Cholesterol: 108.6mg, Sodium: 989.5mg, Carbohydrates: 19.5g, Fiber 3.6g, Sugars: 9g, Protein 28.4g

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