If you’re searching for a vibrant, wholesome meal that’s bursting with flavor and colors, look no further than this Chicken Fajita Spaghetti Squash Bowls Recipe. It’s a delightful twist on classic fajitas, swapping out the usual tortillas for tender, naturally low-carb spaghetti squash. Every bite offers a wonderful mix of tender chicken, caramelized veggies, and melty cheddar cheese that’s baked right inside the squash bowls—making it as satisfying to look at as it is to eat. This recipe is perfect for when you want something comforting, fresh, and just a bit different to impress family and friends.

Ingredients You’ll Need
Gathering these simple yet essential ingredients is the first step toward creating a colorful and delicious dish. Each component plays its part in building bold flavors, appealing textures, and that fantastic balance between zesty and savory that makes the Chicken Fajita Spaghetti Squash Bowls Recipe so irresistible.
- Spaghetti squash: The natural “bowl” and base of the dish, offering a light, spaghetti-like texture when cooked.
- Chicken (cubed): Provides hearty protein, perfectly seasoned to soak up all those Mexican-inspired spices.
- Cumin: Adds a warm, earthy depth that’s essential in fajita seasoning.
- Chili powder: Brings a mild heat and vibrant red color.
- Onion powder: Offers a subtle sweetness that complements the fresh onion slices.
- Garlic powder and crushed garlic: Two layers of garlicky goodness to enhance every bite.
- Salt and pepper: The basics, but crucial for balancing all other flavors.
- Cayenne pepper: A dash to add an exciting kick and warmth.
- Olive oil: Used for roasting squash, sautéing veggies, and flavor-packed marinade.
- Lime juice: Adds a bright, citrusy zing to lift the flavor profile.
- Bell peppers (sliced): Colorful and sweet, they caramelize beautifully for that signature fajita taste.
- Sweet onion (sliced): Softens and browns to create layers of sweetness and texture.
- Salsa: Incorporates tanginess and moisture, binding the filling together.
- Cheddar cheese: Melted inside the bowl for a gooey, cheesy finish.
How to Make Chicken Fajita Spaghetti Squash Bowls Recipe
Step 1: Preparing the Spaghetti Squash
Start by preheating your oven to 425 degrees. Take the spaghetti squash halves, drizzle each cut side with olive oil, then sprinkle salt and pepper evenly. Placing them cut side down on a foil-lined baking sheet helps the squash roast to tender, stringy perfection in about 50 minutes. This step lays the foundation for your edible bowl, so roasting until soft is key.
Step 2: Mixing the Seasonings
While the squash roasts, combine cumin, chili powder, onion powder, garlic powder, salt, pepper, and a pinch of cayenne pepper in a small bowl. This mixture is the secret behind the vibrant, bold flavor that makes the chicken and veggies sing in this Chicken Fajita Spaghetti Squash Bowls Recipe. You can also simplify by using a gluten-free taco seasoning packet if you prefer.
Step 3: Marinating the Chicken
In a gallon-sized Ziploc bag, toss your cubed chicken with the olive oil, lime juice, and the seasoning mix. Ensure every piece is well-coated. Marinating lets the chicken absorb those Southwest-inspired notes and stay juicy and tender when cooked. Pop it in the fridge to soak up the flavors while you prepare the rest.
Step 4: Sautéing the Fajita Vegetables
When your squash has about 25 minutes left in the oven, heat a skillet with 2–3 tablespoons of olive oil over medium heat. Add sliced bell peppers, sweet onion, crushed garlic, salt, and pepper. Keep stirring for 16-18 minutes until the veggies turn beautifully caramelized with golden brown edges—that mix of sweet and savory is absolutely irresistible.
Step 5: Cooking the Chicken
As the squash continues to roast, heat another skillet to medium and cook your marinated chicken. Avoid adding too much marinade to the pan to prevent steaming rather than sautéing. Cook for about 10 minutes until the chicken is no longer pink, and make sure to drain any excess liquid. This step locks in flavor and gives you tender, perfectly cooked meat for your bowls.
Step 6: Combining Chicken, Veggies, Salsa, and Cheese
Once chicken and vegetables are ready, combine both in the larger skillet. Stir in the salsa and half of the cheddar cheese (¾ cup). This blend of juicy chicken, smoky-sweet veggies, tangy salsa, and melty cheese is what truly transforms this into a Chicken Fajita Spaghetti Squash Bowls Recipe worth making again and again.
Step 7: Filling and Baking the Squash Bowls
Take your roasted spaghetti squash out of the oven and gently scrape the strands to create room for the filling. Spoon half of the chicken fajita mixture into each squash half—don’t worry if not all fits perfectly; you can scoop some squash out to make space. Top each filled squash with the remaining cheese and pop them back in the hot oven for 5 minutes, allowing the cheese to melt and brown enticingly.
Step 8: Final Touches and Serving
After baking, your Chicken Fajita Spaghetti Squash Bowls Recipe is ready to enjoy. Add some fresh green onions and extra salsa on top if you like, bringing bright color and extra flavor with every bite. Serve while warm for the ultimate comforting experience.
How to Serve Chicken Fajita Spaghetti Squash Bowls Recipe
Garnishes
Adding garnishes like chopped green onions, fresh cilantro, or a dollop of sour cream can elevate your fajita bowls from tasty to next-level delicious. These fresh elements add brightness and contrast that perfectly complement the rich, cheesy, and spiced filling.
Side Dishes
While the Chicken Fajita Spaghetti Squash Bowls Recipe is hearty on its own, pairing it with a crisp side salad or some black beans gives your meal an added punch of nutrition and texture. Consider a chilled corn salad or simple avocado slices for a cool balance to the warm, spicy filling.
Creative Ways to Present
To wow your guests, serve the squash halves on colorful plates or wooden trays, and surround them with small bowls of salsa, guacamole, and lime wedges. You can also hollow out the squash ahead of time and stuff it buffet-style for a fun, interactive dinner party presentation.
Make Ahead and Storage
Storing Leftovers
You can store any leftover chicken fajita filling separately or keep filled squash halves wrapped tightly in the refrigerator for up to 3 days. Keep the cheese topping fresh by adding it right before reheating when possible to avoid it becoming rubbery.
Freezing
This dish freezes best if you store the chicken fajita filling alone in an airtight container. When ready to eat, thaw overnight in the fridge and reheat before stuffing fresh roasted squash. Freezing filled squash can make the texture a bit watery, so I recommend assembling after reheating the filling.
Reheating
For the best texture, reheat your chicken fajita filling gently in a pan over medium heat, stirring occasionally until warmed through. If you have leftover filled squash, reheat in the oven at 350 degrees until heated fully and cheese is melty. Avoid microwaving to keep the squash texture intact.
FAQs
Can I use a different type of squash instead of spaghetti squash?
While spaghetti squash is ideal because of its stringy texture resembling noodles, you can experiment with other winter squashes like acorn or delicata. Keep in mind the texture and cooking times vary, so the unique appeal of this Chicken Fajita Spaghetti Squash Bowls Recipe might change slightly.
Is this recipe gluten-free?
Yes, this entire Chicken Fajita Spaghetti Squash Bowls Recipe is naturally gluten-free, especially if you use a gluten-free taco seasoning packet. It’s a perfect choice for those watching gluten intake without compromising flavor.
Can I make this recipe vegetarian?
Absolutely! Substitute the chicken with hearty vegetables like mushrooms, zucchini, or seasoned tofu. The fajita spices and toppings will keep the dish flavorful and satisfying even without chicken.
How spicy is this recipe?
The heat level is moderate due to the cayenne and chili powder but can be easily adjusted. Omit the cayenne or use mild chili powder to reduce spice, or add extra if you like it hot. The cheese and salsa help balance out any heat nicely.
Can I prepare parts of this recipe ahead of time?
Yes! You can roast the spaghetti squash and marinate the chicken a day ahead. The filling can be sautéed and combined in advance too, making dinner a breeze on busy nights when you just have to assemble and bake.
Final Thoughts
This Chicken Fajita Spaghetti Squash Bowls Recipe is one of those dishes that feels like a warm hug and a fiesta all at once. It’s fresh, healthy, and packed with flavors that will quickly make it a household favorite. Whether you’re cooking for family, friends, or simply treating yourself, this recipe is worth every delicious bite. Give it a try and watch everyone fall in love with its vibrant charm and comforting goodness!
Print
Chicken Fajita Spaghetti Squash Bowls Recipe
- Prep Time: 30 minutes
- Cook Time: 55 minutes
- Total Time: 1 hour 25 minutes
- Yield: 6 servings
- Category: Main Course
- Method: Baking
- Cuisine: Mexican-American
- Diet: Gluten Free
Description
This Chicken Fajita Spaghetti Squash Bowl recipe combines the flavors of classic fajitas with a healthy twist by using roasted spaghetti squash as a base. Tender, marinated chicken and caramelized bell peppers and onions are mixed with salsa and cheddar cheese, then baked together for a satisfying, low-carb meal that serves 6.
Ingredients
Spaghetti Squash
- 1 spaghetti squash (cut in half length-wise, seeds removed)
Chicken & Marinade
- 1 pound chicken (raw, cut into 1-inch cubes)
- 1 teaspoon cumin
- 1 teaspoon chili powder
- ¼ teaspoon onion powder
- ¼ teaspoon garlic powder
- ¼ teaspoon salt
- ¼ teaspoon pepper
- 1/8 teaspoon cayenne pepper
- 3 tablespoons olive oil
- 2 tablespoons lime juice
Vegetables & Sauté
- 2 bell peppers (sliced into thin 2-inch long slices)
- 1 sweet onion (sliced into thin 2-inch long slices)
- 2 cloves garlic (crushed)
- 2–3 tablespoons olive oil (for sautéing)
- ½ teaspoon salt
- ½ teaspoon pepper
Other Ingredients
- ¾ cup salsa (plus extra for topping)
- 1 ½ cups cheddar cheese (divided into two ¾ cup portions)
- 1 tablespoon olive oil (for drizzling)
Instructions
- Preheat Oven: Preheat your oven to 425°F (220°C) to prepare for roasting the spaghetti squash.
- Prepare Squash: Drizzle 1 tablespoon of olive oil inside each spaghetti squash half (with seeds removed), then sprinkle salt and pepper evenly. Rub the oil and seasoning all over the inner surface.
- Roast Squash: Place the squash halves cut-side down on a baking sheet lined with aluminum foil and bake for 50 minutes until tender.
- Mix Seasonings: In a small bowl, combine cumin, chili powder, onion powder, garlic powder, salt, pepper, and cayenne pepper. Alternatively, use a gluten-free taco seasoning packet if preferred.
- Make Marinade: Add 3 tablespoons olive oil and 2 tablespoons lime juice to the seasoning mix and stir until well combined.
- Marinate Chicken: Place cubed chicken in a gallon-sized Ziploc bag, pour in the marinade, and toss to coat the chicken evenly. Refrigerate until ready to cook.
- Sauté Vegetables: When the squash has about 25 minutes left, heat 2 to 3 tablespoons olive oil in a skillet over medium heat. Add sliced bell peppers, onion, crushed garlic, salt, and pepper. Sauté for 16-18 minutes, stirring constantly until the veggies are caramelized and golden brown.
- Cook Chicken: When the squash has about 15 minutes remaining, heat another skillet over medium heat and add marinated chicken (draining excess marinade). Cook for 10 minutes or until fully cooked, stirring regularly and draining excess liquid while cooking.
- Combine Filling: Mix the cooked chicken and sautéed vegetables in the larger skillet. Add ¾ cup salsa and ¾ cup cheddar cheese and stir well until everything is combined and the cheese begins to melt.
- Assemble Bowls: Remove the roasted spaghetti squash from the oven and evenly divide half of the chicken and vegetable mixture into each squash half. If needed, remove some squash strands to fit all the filling.
- Add Cheese & Bake: Top each bowl with the remaining ¾ cup cheddar cheese. Return to the oven and bake at 425°F for an additional 5 minutes until the cheese melts and starts to brown slightly.
- Serve: Garnish the bowls with green onions and extra salsa if desired. Serve warm and enjoy your flavorful Chicken Fajita Spaghetti Squash Bowls!
Notes
- You can substitute the homemade spice mix with a gluten-free taco seasoning packet for convenience.
- Be careful not to add too much marinade when cooking chicken to prevent sogginess.
- Caramelizing vegetables slowly develops deep flavor—stir constantly to avoid burning.
- To make the filling fit easily, remove some of the roasted spaghetti squash strands if necessary.
- Leftover filling can be stored separately and reheated for quick meals.
- If you don’t have cheddar cheese, a Mexican cheese blend or Monterey Jack can be used as alternatives.

