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If you’re craving a vibrant meal that bursts with flavor while keeping things light and wholesome, this Chicken Fajita Spaghetti Squash Bowls Recipe is an absolute must-try. Imagine tender cubes of seasoned chicken paired with sweet caramelized bell peppers and onions, all nestled inside a naturally gluten-free spaghetti squash “bowl,” then topped with melted cheddar cheese and a zing of fresh salsa. It’s colorful, comforting, and endlessly satisfying without any heaviness, making it a fantastic weeknight dinner that feels like a celebration on a plate.

Ingredients You’ll Need

These simple yet essential ingredients come together to create a perfect balance of flavors and textures. Each item plays a key role—from the tender chicken and vibrant bell peppers adding heart and color, to the spaghetti squash’s delicate strands serving as a nutritious, grain-free base.

  • 1 spaghetti squash (cut in half length-wise, seeds removed): Acts as a naturally low-carb, gluten-free bowl with spaghetti-like strands inside.
  • 1 pound chicken (cubed into 1-inch pieces): The hearty protein star of the dish, perfect for soaking up spices.
  • 1 teaspoon cumin: Adds a warm, earthy aroma that’s fundamental to fajita flavors.
  • 1 teaspoon chili powder: Brings a smoky, mildly spicy kick to the chicken seasoning.
  • ¼ teaspoon onion powder: Enhances the savory depth without overpowering.
  • ¼ teaspoon garlic powder: A subtle punch of garlic that melds beautifully with other spices.
  • ¼ teaspoon salt: Balances all the flavors perfectly.
  • ¼ teaspoon pepper: Adds gentle heat and a touch of complexity.
  • 1/8 teaspoon cayenne pepper: A little spark of heat to elevate the fajita seasoning.
  • 3 tablespoons olive oil: Used for marinating and cooking, bringing richness and moisture.
  • 2 tablespoons lime juice: Injects brightness and a refreshing tang to the marinade.
  • 2 bell peppers (sliced into thin 2-inch strips): Provide sweet crunch and beautiful color contrast.
  • 1 sweet onion (sliced thinly into 2-inch strips): Slowly caramelizes for a luscious, mellow sweetness.
  • 2 cloves garlic (crushed): Fresh garlic flavor that complements the veggies perfectly.
  • 2-3 tablespoons olive oil: For sautéing the vegetables to caramelized perfection.
  • ½ teaspoon salt: Enhances the natural flavors of the sautéed veggies.
  • ½ teaspoon pepper: Adds a mild heat to the vegetables.
  • ¾ cup salsa (+ extra for topping): Adds a fresh, zesty touch and moisture to the filling.
  • 1 ½ cups cheddar cheese (divided into ¾ cup portions): Melts creamy and golden, offering that perfect cheesy finish.

How to Make Chicken Fajita Spaghetti Squash Bowls Recipe

Step 1: Prepare and Roast the Spaghetti Squash

Begin by preheating your oven to 425 degrees. Drizzle olive oil inside the squash halves, then sprinkle salt and pepper evenly before rubbing it all over the surface. Place them cut-side down on an aluminum foil lined baking sheet and roast for about 50 minutes. This slow roasting softens the squash and creates those delightful spaghetti-like strands that are the base for this dish.

Step 2: Mix the Fajita Seasonings

In a small bowl, combine cumin, chili powder, onion powder, garlic powder, salt, pepper, and cayenne pepper. This blend is the heart of the chicken’s bold fajita flavor. If you’re short on time or ingredients, feel free to substitute with your favorite gluten-free taco seasoning packet—it’s a convenient shortcut that still packs a punch.

Step 3: Marinate the Chicken

Add your olive oil and lime juice to the seasoning mix to create a zesty marinade. Toss the cubed chicken in this mixture inside a gallon-sized Ziploc bag, making sure every piece is well-coated. Pop it into the fridge while the squash roasts to let those flavors sink in beautifully.

Step 4: Sauté the Vegetables

With roughly 25 minutes left on the squash’s timer, heat 2 to 3 tablespoons of olive oil in a skillet over medium heat. Add the sliced bell peppers, sweet onion, crushed garlic, and season with salt and pepper. Stir continuously for 16 to 18 minutes until the veggies soften and develop a gorgeous golden-brown caramelization that’s sweet and savory.

Step 5: Cook the Marinated Chicken

About 15 minutes before the squash is ready, warm a second skillet to medium heat and cook the chicken cubes. Be mindful not to pour too much marinade into the pan; cook until the chicken is fully cooked and golden, about 10 minutes, draining excess liquid as needed. This method ensures juicy, flavorful chicken that complements the veggies perfectly.

Step 6: Combine Chicken, Veggies, Salsa, and Cheese

Transfer the cooked chicken to the skillet holding the veggies and stir in salsa along with ¾ cup of cheddar cheese. Mix everything thoroughly so the cheese melts through the filling, creating a creamy, saucy mixture bursting with those signature fajita flavors.

Step 7: Assemble the Chicken Fajita Spaghetti Squash Bowls Recipe

Once your roasted squash is done, carefully flip the halves cut-side up. Scoop generous portions of the chicken and veggie filling into each half. If necessary, you can trim some squash fibers to fit more filling—the deliciousness is worth it! Top each bowl with the remaining cheddar cheese for that irresistible melty blanket.

Step 8: Final Bake and Serve

Pop the filled squash bowls back in the oven at 425 degrees and bake for an extra 5 minutes or until the cheese turns bubbly and golden brown on top. This last step adds an incredible finishing touch that will have everyone eager to dig in. Serve warm, optionally garnished with green onions and extra salsa for an added pop of freshness.

How to Serve Chicken Fajita Spaghetti Squash Bowls Recipe

Garnishes

Fresh green onions or chopped cilantro brighten the dish with vibrant color and fresh, sharp notes that contrast wonderfully with the warm, cheesy filling. A dollop of extra salsa or a squeeze of lime juice can elevate each bite with a touch of acidity and zing.

Side Dishes

This recipe shines on its own, but if you want to round out your meal, consider a light side salad with avocado or a simple Mexican street corn salad. A side of black beans or cilantro-lime rice can also add an extra layer of heartiness and make the feast even more satisfying.

Creative Ways to Present

Serving the filling inside the spaghetti squash halves is already stunning, but for a fun twist, you can shred the squash strands fully and mix them with the chicken fajita filling in a large casserole dish, then bake. Alternatively, turn the filling into fajita-stuffed bell peppers for a colorful, hand-held option. The Chicken Fajita Spaghetti Squash Bowls Recipe opens the door to lots of playful presentation ideas!

Make Ahead and Storage

Storing Leftovers

Leftover filled squash halves can be tightly wrapped and stored in the refrigerator for up to 3 days. This makes them excellent for quick meals later in the week when you want a hassle-free, flavorful dinner in minutes.

Freezing

For longer-term storage, cool the cooked ingredients completely before assembling. Portion the chicken fajita filling and cooked spaghetti squash separately into airtight containers or freezer bags. Freeze for up to 3 months. Avoid freezing fully assembled squash bowls since the texture of the squash may change after thawing.

Reheating

When ready to enjoy leftovers, thaw overnight in the refrigerator. Reheat filling separately in a skillet or microwave until warm, then spoon back into reheated squash halves. This method preserves the best texture and flavor, allowing you to enjoy the Chicken Fajita Spaghetti Squash Bowls Recipe just as much the second time around!

FAQs

Can I use a different type of squash?

While spaghetti squash works best because of its stringy texture, you could experiment with delicata or acorn squash for a slightly different taste and texture, though these won’t mimic “spaghetti” strands exactly.

Is this recipe gluten-free and keto-friendly?

Yes! Using spaghetti squash instead of pasta makes this recipe naturally gluten-free and low in carbs, making it a great choice for keto and gluten-free diets.

Can I make this recipe vegetarian?

Absolutely! Swap the chicken for hearty sautéed mushrooms, tofu, or tempeh, and you’ll have a delicious vegetarian-friendly meal that still captures the spirit of the fajita flavors.

How spicy is the Chicken Fajita Spaghetti Squash Bowls Recipe?

The heat level is mild to moderate thanks to the cayenne pepper and chili powder. You can always adjust the spice to your preference by reducing or increasing the cayenne, or adding fresh jalapeños for more kick.

What’s the best way to cut and prepare spaghetti squash?

Cut the squash lengthwise with a large, sharp knife and scoop out seeds using a spoon. Drizzle with oil and season well before roasting to bring out its natural sweetness and make the strands easy to separate once cooked.

Final Thoughts

I truly hope you enjoy making and savoring the Chicken Fajita Spaghetti Squash Bowls Recipe as much as I do. It’s the kind of dish that feels special without fuss, bursting with layers of flavor, and packed with colorful, wholesome ingredients. Once you try it, this recipe will no doubt earn a permanent spot in your meal rotation!

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Chicken Fajita Spaghetti Squash Bowls Recipe

5 Stars 4 Stars 3 Stars 2 Stars 1 Star 4.1 from 86 reviews
  • Author: admin
  • Prep Time: 30 minutes
  • Cook Time: 50 minutes
  • Total Time: 1 hour 20 minutes
  • Yield: 6 servings
  • Category: Main Course
  • Method: Baking
  • Cuisine: Mexican-American
  • Diet: Gluten Free

Description

These Chicken Fajita Spaghetti Squash Bowls are a flavorful, low-carb twist on classic fajitas, served inside roasted spaghetti squash halves. Tender, cumin and chili spiced chicken cubes pair perfectly with caramelized bell peppers, onions, and a touch of salsa, topped with melted cheddar cheese. This dish offers a deliciously healthy way to enjoy fajita flavors with a nutritious vegetable base.


Ingredients

Scale

Spaghetti Squash and Seasoning

  • 1 spaghetti squash (cut in half lengthwise, seeds removed)
  • ¼ teaspoon salt
  • ¼ teaspoon pepper
  • 1 tablespoon olive oil (for squash)
  • 1 tablespoon olive oil (for squash)

Chicken and Marinade

  • 1 pound chicken, 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 and Cooking

  • 2 bell peppers, sliced into thin 2-inch long slices
  • 1 sweet onion, sliced into thin 2-inch long slices
  • 2 cloves garlic, crushed
  • 23 tablespoons olive oil (for sautéing veggies)
  • ½ teaspoon salt
  • ½ teaspoon pepper

Additional Ingredients

  • ¾ cup salsa, plus extra for topping
  • 1½ cups cheddar cheese, divided into two ¾ cup portions


Instructions

  1. Preheat and prepare squash: Preheat oven to 425°F (220°C). Drizzle 1 tablespoon olive oil on the inside of each spaghetti squash half and sprinkle with ¼ teaspoon salt and ¼ teaspoon pepper. Rub the seasoning thoroughly over the entire cut surface.
  2. Bake spaghetti squash: Place the squash halves cut side down on an aluminum foil-lined baking sheet. Bake for 50 minutes until squash is tender and easily shredded with a fork.
  3. Mix chicken seasoning: In a small bowl, combine cumin, chili powder, onion powder, garlic powder, ¼ teaspoon salt, ¼ teaspoon pepper, and cayenne pepper. Stir well to combine. Alternatively, a gluten-free taco seasoning packet can be used.
  4. Prepare marinade: Add 3 tablespoons olive oil and lime juice to the seasoning mix and stir until combined.
  5. Marinate chicken: Place cubed chicken in a gallon-sized Ziploc bag. Pour in the marinade and toss until all pieces are fully coated. Refrigerate until ready to cook.
  6. Sauté vegetables: When the squash has about 25 minutes remaining, heat 2-3 tablespoons olive oil in a skillet over medium heat. Add bell peppers, onion, garlic, ½ teaspoon salt, and ½ teaspoon pepper. Sauté for 16-18 minutes, stirring frequently until vegetables are caramelized and golden brown.
  7. Cook chicken: With about 15 minutes left on the squash, heat another skillet (preferably cast iron) over medium heat. Add marinated chicken, avoiding excess marinade. Cook for approximately 10 minutes until thoroughly cooked through, draining any liquid as you go.
  8. Combine chicken and veggies: Add cooked chicken and sautéed vegetables to the larger skillet. Stir in ¾ cup salsa and ¾ cup cheddar cheese. Mix everything well to combine and warm through.
  9. Fill squash bowls: Remove spaghetti squash from oven. Use a fork to gently shred the squash flesh if desired. Divide the chicken fajita mixture evenly between the two squash halves. Remove some squash flesh if needed to make room for all the filling.
  10. Top with cheese and bake: Sprinkle the remaining ¾ cup cheddar cheese over the stuffed squash halves. Return to the oven and bake for an additional 5 minutes at 425°F, or until cheese is melted and slightly browned.
  11. Serve: Remove from oven and optionally garnish with chopped green onions and extra salsa. Serve warm and enjoy your healthy, flavorful meal!

Notes

  • Using a gluten-free taco seasoning packet is a convenient substitute for the custom seasoning mix.
  • Carefully drain chicken liquid during cooking to prevent sogginess.
  • Caramelizing the vegetables adds a rich depth of flavor; don’t rush this step.
  • If the filling mixture is too large, you can scoop out some squash flesh to fit everything in the bowl.
  • Leftovers can be stored in an airtight container in the refrigerator for up to 3 days.
  • This recipe is naturally low-carb and gluten-free by using spaghetti squash instead of traditional pasta or tortillas.

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