This crowd-pleasing casserole brings cheesy, low-carb goodness to the table in a protein-packed, one-pan meal!

Spaghetti squash is a true culinary wonder. It looks like a vegetable but cooks up like pasta. And it adds serious nutrition to every dish it graces. Take this BBQ baked chicken spaghetti squash casserole as a prime example. It could easily be a pasta-filled carbo-loader’s fantasy—but the squash makes it lighter, brighter, and way tastier while fully supporting its protein-forward profile.
I love making this casserole when I have leftover chicken. Whether we grilled the day before or I roasted a whole bird that didn’t get picked clean, starting with cooked chicken gives me a head start. Once the chicken, squash, and onions meld into the cheese and spices, they develop a deeply satisfying savory flavor profile. I typically use a sugar-free barbecue sauce to keep it from getting too sweet—and one of these days I might cross over into making my own BBQ sauce from scratch. Until that day, I’ll enjoy the convenience of a store-bought bottle that skips the added sugar.
Roasting the spaghetti squash is the only time-consuming part of this recipe. But I use that time to prep all the other ingredients, so I’m ready to assemble the casserole as soon as it’s done. Then I’ve got a full half hour to clean up my kitchen while the dish bakes—and I get to enjoy dinner with a clean conscience!
If my gluten-free niece is joining us—or I’m making this ahead to take to a potluck—I just skip the panko breadcrumbs. And occasionally I’ll toss in red bell peppers or spinach for extra color. This casserole is a definite crowd-pleaser that makes for crave-worthy leftovers!

Is BBQ Baked Chicken Spaghetti Squash Casserole Healthy?
This casserole is a nutrient-dense, high-protein, and relatively low-calorie dish that can fit into many healthy eating plans. The use of spaghetti squash instead of pasta keeps the carbs lower and adds fiber, vitamins, and minerals. Greek yogurt boosts the protein and adds creaminess with less fat than traditional sour cream or mayonnaise. However, the dish is moderately high in sodium and sugar, largely due to the barbecue sauce and cheese.
For those keeping an eye on their salt, sugar, or fat intake, consider using less cheese and opting for a reduced-sodium, low-sugar barbecue sauce—or make your own from one of these barbecue sauce recipes. Make this dish gluten-free by omitting the breadcrumbs or choosing gluten-free panko crumbs. Make it Paleo-friendly by subbing in unsweetened coconut yogurt for the Greek yogurt, using a Paleo-approved barbecue sauce, and skipping the cheese and panko.

Casserole Math: The Formula For A Cozy Meal
At its core, every great casserole follows a simple equation: Base + Protein + Veggies + Binder + Seasoning + Topping. In this BBQ baked chicken spaghetti squash casserole, the spaghetti squash acts as the base, shredded chicken provides protein, onions and cilantro add veggie freshness, Greek yogurt and cheese work as binders for creaminess, spices and barbecue sauce deliver bold flavor, and a sprinkle of panko gives that irresistible golden crunch on top. Once you understand this formula, you can mix and match ingredients based on what you have on hand, your dietary needs, or your flavor cravings.
This formula empowers you to get creative in the kitchen. Swap out the spaghetti squash for cooked rice, quinoa, or even roasted sweet potatoes as your base. Try black beans, tofu, or lentils for a vegetarian protein option. Use whatever veggies are in season, and experiment with different binders like cottage cheese, dairy-free yogurt, or even a simple egg mixture. Change up the seasonings to go from American barbecue to Italian, Mexican, or Mediterranean vibes. Top it all off with nuts, seeds, or gluten-free crumbs for texture. With this formula, you can turn just about any leftovers or pantry staples into a hearty, satisfying casserole that’s uniquely yours!
How Do I Store Leftovers?
This casserole keeps well in the fridge for up to 4 days and in the freezer for up to 3 months. Thaw overnight in the fridge. If it’s a little watery after thawing, drain off the excess liquid before reheating. The best reheating method is in a preheated 350°F, covered with foil, for 20–25 minutes. I like to add more freshly shredded cheese in the final 5 minutes. You can also microwave individual portions on medium power in 1-minute intervals, stirring and checking for even heating as you go.

Serving Suggestions
Serve this BBQ baked chicken spaghetti squash casserole with something light and fresh, like a Spring Salad or this Keto Salad. It also goes well with warm sides, like Crock-Pot Green Beans and Roasted Zucchini And Squash. Add some Keto Flatbread for sopping up every last bit of barbecue sauce—and don’t forget dessert, like a sweet Lemon Meringue Pie or an adorable Mini Fruit Tart.
Recipe
Ingredients
- 2.5 cups spaghetti squash about 1/2 a medium-sized squash
- 2 cups shredded chicken breast about 1 medium-sized breast
- 1/2 red onion chopped
- 1/4 cup green onion
- 1/4 cup cilantro
- 1/2 teaspoon salt
- 1/8 teaspoon pepper
- 1/4 teaspoon chile powder
- 1/4 teaspoon cumin powder
- 1/4 teaspoon garlic powder
- 1/4 teaspoon paprika
- 1/4-1/2 teaspoon red pepper flakes
- 3/4 cup reduced-fat cheddar cheese grated and divided
- 1/2 cup barbecue sauce of choice
- 6 tablespoons plain fat-free Greek yogurt
- 2 tablespoons gluten-free panko crumbs
Instructions
Prep The Casserole Ingredients
- Preheat oven to 400°F.
- Cut the spaghetti squash in half and scoop out the seeds and strings. Place it face down on a baking sheet. Bake it until it is fork-tender, about 40 minutes.
- Bring a medium-sized pot of salted water to a boil. Boil the chicken breast until cooked through, about 20-25 minutes. Set aside to cool.
- While your chicken and squash are cooking, heat a grill pan over high heat. Cook the chopped red onions until they have nice grill marks, about 5 minutes. Set aside.
- Chop the green onion and cilantro. Set aside.
- Remove the fully cooked squash from the oven. Use a fork to scrape the flesh out of the skin and into a bowl. It will come out in the form of long, pasta-like strands.
Assemble The Casserole:
- Spray a casserole dish or cast-iron skillet with cooking spray.
- Using 2 forks, shred the chicken into small pieces. Place them in a large bowl.
- Add the spaghetti squash, grilled red onion, green onion, cilantro, salt, pepper, chile powder, cumin, garlic, paprika, red pepper flakes and 1/2 cup of the cheddar cheese.
- In a medium-sized bowl, combine the barbecue sauce and Greek yogurt
- Pour the yogurt mixture over the squash mixture. Mix gently until all ingredients are well combined.
- Pour the mixture into the prepared casserole dish. Top with the panko crumbs and remaining cheddar cheese.
Bake The Casserole:
- Bake at 400°F for 25 minutes. Turn oven to high broil. Broil until the topping is brown and bubbly, about 5 minutes.
- Let casserole cool on the counter for a few minutes before serving.
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