If you’re craving a dish that’s both comforting and bursting with fresh, vibrant flavors, you’re going to love this Baked Pesto Chicken Spaghetti Squash. It combines tender, shredded chicken with the bright, herby essence of basil pesto, all nestled inside the naturally sweet and stringy flesh of roasted spaghetti squash. It’s a lighter yet satisfying alternative to traditional pasta casseroles and perfect for anyone looking to enjoy hearty, wholesome meals without skimping on taste. Plus, it’s baked to bubbly, cheesy perfection, making every bite an irresistible melody of texture and flavor.

Baked Pesto Chicken Spaghetti Squash Recipe - Recipe Image

Ingredients You’ll Need

To make this dish truly shine, the ingredients are simple but each plays a crucial role in creating that perfect balance of taste, texture, and color. From the creamy cheeses to the spicy kick of red pepper flakes, every component elevates the Baked Pesto Chicken Spaghetti Squash into a mouthwatering experience.

2 medium spaghetti squash: The star vegetable that provides a natural noodle alternative with a slightly sweet flavor and satisfying texture.
1 tbsp olive oil: Helps roast the squash to a tender finish while adding a subtle fruitiness.
Salt and pepper: Essential for seasoning and bringing all the flavors together.
3 cups shredded chicken: Offers lean protein and a tender base to soak up all the savory pesto and cheese.
3/4 cup mozzarella cheese (grated plus extra for topping): Adds a gooey, melt-in-your-mouth cheesy layer that makes this dish so comforting.
1/4 cup parmesan cheese (grated): Brings a sharp, nutty complexity that pairs perfectly with pesto.
3/4 cup basil pesto: The vibrant, herbaceous heart of the recipe, infusing each bite with fresh basil, garlic, and pine nut flavors.
1/2 tsp red pepper flakes: Adds a subtle heat that balances the richness of the cheeses and pesto.

How to Make Baked Pesto Chicken Spaghetti Squash

Step 1: Prep and Roast the Spaghetti Squash

Start by preheating your oven to 400 degrees Fahrenheit. Cut each spaghetti squash in half and scoop out the seeds—this step is simple but essential so the squash roasts evenly. Drizzle the cut sides with olive oil and sprinkle with salt and pepper, then place them cut-side down on a baking sheet. Roast for about 45 minutes until the flesh is tender and can be easily shredded with a fork. This roasting creates the perfect texture to mimic spaghetti noodles and brings out the squash’s natural sweetness.

Step 2: Combine the Pesto Chicken Mixture

While the squash roasts, mix together shredded chicken, mozzarella, parmesan, basil pesto, and red pepper flakes in a large bowl. This combination gives the dish its rich, creamy, and flavorful base. The pesto keeps the chicken moist and adds a fresh punch, while the cheeses lend gooeyness and depth, with the pepper flakes bringing just the right kick.

Step 3: Scrape and Mix Squash with Pesto Chicken

Once the squash is cooked and cool enough to handle, gently scrape the flesh with a fork to create noodle-like strands. Add this “spaghetti” to the bowl with your pesto chicken mixture, then toss everything together until fully combined. This step ensures every bite will be loaded with pesto-infused squash and tender chicken.

Step 4: Assemble and Bake

Divide the mixture evenly back into each spaghetti squash half. Sprinkle extra mozzarella or parmesan on top for that irresistible melted cheese finish. Pop them back into the oven for about 5 minutes, just enough time to melt the cheese and bind all the flavors together beautifully.

How to Serve Baked Pesto Chicken Spaghetti Squash

Garnishes

A sprinkle of red pepper flakes enhances the dish’s gentle heat, and a few twists of fresh black pepper add an aromatic touch right before serving. If you have fresh basil leaves on hand, tear a few on top for an extra pop of herbal brightness and vibrant green color that makes the dish look as good as it tastes.

Side Dishes

Keep it light with a simple arugula salad dressed in lemon vinaigrette or roast some garlic green beans for a bit of crunch. Garlic bread or a warm whole-grain roll work wonderfully if you want to round out this meal with something carb-packed and comforting. The versatility of Baked Pesto Chicken Spaghetti Squash means it pairs well with anything fresh and green or toasty and buttery.

Creative Ways to Present

For a stunning presentation, serve the pesto chicken spaghetti squash in the roasted squash shells, which adds rustic charm to your plate. You could also stuff the mixture into hollowed bell peppers or zucchini boats for a delightful twist. For a family-style meal, transfer everything to a large casserole dish and bake until bubbly on top, perfect for feeding a crowd or meal prepping.

Make Ahead and Storage

Storing Leftovers

Place any leftovers in an airtight container and refrigerate for up to 3 days. The flavors actually deepen as it sits, making your next meal just as delicious and simple to reheat.

Freezing

You can freeze the Baked Pesto Chicken Spaghetti Squash either assembled or as the pesto chicken mixture alone. Store in freezer-safe containers for up to 2 months. Thaw overnight in the fridge before reheating to maintain the best texture and flavor.

Reheating

Reheat leftovers gently in the oven at 350 degrees Fahrenheit uncovered for 15–20 minutes until warmed through, or microwave individual portions for 2–3 minutes. Adding a splash of water before reheating helps keep the squash from drying out.

FAQs

Can I make this recipe vegetarian?

Absolutely! Simply skip the chicken and add more roasted veggies like mushrooms, zucchini, or artichokes to keep it hearty and flavorful while sticking to a vegetarian diet.

Is spaghetti squash difficult to cook?

Not at all. Roasting spaghetti squash is straightforward and hands-off—just make sure to cut it carefully and roast until tender. The flesh easily scrapes into noodles that can replace pasta in so many dishes.

Can I use store-bought pesto?

Yes, store-bought pesto works just fine and saves time. However, homemade pesto with fresh basil will add a brighter flavor if you have the time to whip some up.

What if I don’t have red pepper flakes?

You can omit them entirely or substitute with a pinch of cayenne pepper or a few dashes of hot sauce to add your preferred level of heat.

Is this recipe gluten-free?

Yes, since spaghetti squash is naturally gluten-free and none of the other ingredients contain gluten, this recipe is safe for those avoiding gluten.

Final Thoughts

This Baked Pesto Chicken Spaghetti Squash is one of those special meals that feels like a hug on a plate—comforting, flavorful, and fresh all at once. I encourage you to give this recipe a try the next time you want something wholesome yet indulgent. It’s a brilliant way to enjoy the best of seasonal veggies with beloved classic flavors, and once you try it, I promise it will become a favorite in your kitchen, just like it is in mine.