If you are craving a vibrant, flavorful, and wholesome meal that feels both comforting and fresh, this Chicken Fajita Spaghetti Squash Bowls Recipe is about to become your new go-to. Imagine tender, juicy chicken cubes seasoned with bold, smoky spices, perfectly caramelized bell peppers and onions, all nestled into naturally sweet and nutrient-packed spaghetti squash halves. This dish brings together the best of Mexican-inspired fajita flavors with a clever, low-carb twist that’s as fun to eat as it is delicious. Whether you’re cooking for family or friends, these bowls are a beautiful, colorful feast that will make everyone ask for seconds.

Ingredients You’ll Need
The magic of this recipe lies in its simplicity and the freshness of each ingredient. Every component plays a crucial role: the spaghetti squash provides a tender yet slightly crisp base, the chicken packs protein and flavor, and the spices and veggies create a vibrant aroma and mouthwatering taste that will awaken your senses.
- 1 spaghetti squash (cut in half length-wise, seeds removed): The perfect low-carb vessel with a delicate texture that flakes like spaghetti when cooked.
- 1 pound chicken (raw, cut into 1-inch cubes): Provides juicy, tender protein that soaks up the bold fajita marinade beautifully.
- 1 teaspoon cumin: Adds a warm, earthy undertone essential for authentic fajita flavor.
- 1 teaspoon chili powder: Brings smoky depth and a subtle kick of heat.
- ¼ teaspoon onion powder: Enhances the savory profile without overwhelming.
- ¼ teaspoon garlic powder: Offers a gentle garlic aroma that complements the fresh garlic cloves.
- ¼ teaspoon salt: Balances and elevates all the flavors.
- ¼ teaspoon pepper: Adds mild heat and depth.
- â…› teaspoon cayenne pepper: For a hint of fiery warmth that wakes up your palate.
- 3 tablespoons olive oil: Used in marinades and cooking to deliver richness and keep everything juicy.
- 2 tablespoons lime juice: Adds bright acidity and freshness to the marinade.
- 2 bell peppers (sliced into thin 2-inch strips): Provide vibrant color and sweet crunch when sautéed.
- 1 sweet onion (sliced into thin 2-inch strips): Caramelizes beautifully to create sweet, mellow bites.
- 2 cloves garlic (crushed): Give a punch of fresh garlicky flavor to the veggies.
- 2–3 tablespoons olive oil: Needed for sautéing the vegetables and achieving that perfect caramelization.
- ½ teaspoon salt: To season the sautéed vegetables perfectly.
- ½ teaspoon pepper: Adds a mild peppery note to the vegetables.
- ¾ cup salsa (+ extra for topping): Brings acidity and moisture, tying all the elements together with a zesty burst.
- 1 ½ cups cheddar cheese (divided into ¾ cup portions): Melts over the top for gooey, cheesy indulgence.
How to Make Chicken Fajita Spaghetti Squash Bowls Recipe
Step 1: Roast the Spaghetti Squash
Start by preheating your oven to 425°F. Drizzle olive oil on the cut sides of the squash halves and sprinkle with salt and pepper. Placing the halves cut side down on a foil-lined baking sheet allows the squash to roast evenly, yielding tender strands that mimic pasta but with a wonderfully subtle sweetness. Roast for about 50 minutes until the flesh is easily shredded with a fork.
Step 2: Prepare the Fajita Seasoning and Marinade
Mix all the dry spices—cumin, chili powder, onion powder, garlic powder, salt, pepper, and cayenne—in a bowl. This blend will give your chicken all the smoky, spicy notes that define fajitas. Add olive oil and lime juice to create a vibrant marinade that not only flavors the chicken but also helps keep it juicy during cooking.
Step 3: Marinate the Chicken
Toss the cubed chicken into a gallon-sized Ziplock bag, pour in the marinade, and shake to coat every piece thoroughly. This step is key for infusing your chicken with every bit of that delicious seasoning. Let it rest in the refrigerator while you work on other components.
Step 4: Sauté the Bell Peppers, Onions, and Garlic
About halfway through the squash roasting time, heat olive oil in a skillet and add the sliced peppers, onions, and crushed garlic seasoned with salt and pepper. Stir constantly over medium heat until the veggies begin to caramelize, turning a glorious golden brown. This slow sauté develops deep flavors, transforming simple veggies into something irresistible.
Step 5: Cook the Chicken
In a separate skillet, cook the marinated chicken over medium heat. Avoid adding too much marinade to the pan; drain excess liquid as needed to get a nice sear on your chicken cubes. Cooking for about 10 minutes should ensure the chicken is fully cooked and tender, while still juicy.
Step 6: Combine Filling Ingredients
Once the chicken and veggies are ready, toss them together in the larger skillet with salsa and half of the cheddar cheese. Stir until the cheese is melted and the mixture is beautifully combined—this filling is packed full of juicy, saucy, cheesy goodness that is pure comfort.
Step 7: Stuff the Squash and Bake with Cheese
Remove the spaghetti squash from the oven and use a fork to fluff the flesh gently. Spoon half of the chicken fajita filling into each squash half. It’s okay if not all the filling fits because this dish is all about hearty portions and flavor. Top generously with the remaining cheese, then pop it back in the oven to bake for another 5 minutes until the cheese melts and develops golden brown edges.
How to Serve Chicken Fajita Spaghetti Squash Bowls Recipe
Garnishes
Adding fresh garnishes can brighten the dish further. I love sprinkling chopped green onions or fresh cilantro for a pop of color and an herbal note. A dollop of extra salsa or even a spoonful of sour cream ups the creaminess and tang, making every bite even more luscious.
Side Dishes
These bowls are a satisfying meal on their own, but pairing them with a fresh green salad, some guacamole, or a simple black bean salad complements the fajita flavors perfectly and adds extra texture to your plate. For a heartier occasion, some warm, crusty bread on the side is always a winner.
Creative Ways to Present
Serving the filling in the spaghetti squash itself is already a showstopper, but you can also scoop some out and serve it over a bed of cilantro-lime rice or inside warm tortillas for a fajita-inspired twist on tacos. For parties, consider mini squash boats or even stuffed bell peppers as fun alternatives.
Make Ahead and Storage
Storing Leftovers
You can store any leftover chicken fajita filling and spaghetti squash halves separately in airtight containers in the refrigerator for up to 3 days. This keeps the flavors fresh and the squash from becoming too mushy.
Freezing
The chicken fajita mixture freezes well. Just pack it tightly into a freezer-safe container or bag for up to 3 months. I recommend freezing the squash separately because its texture can become watery after thawing.
Reheating
Warm leftovers gently on the stovetop or in the microwave until heated through. If reheating the stuffed squash, baking it in the oven for 10-15 minutes at 350°F helps maintain the texture of the squash and melts the cheese just right again.
FAQs
Can I use another type of squash instead of spaghetti squash?
Spaghetti squash is unique for its stringy texture that resembles pasta, so if you want to keep that effect, it’s best to stick with it. But you could experiment with butternut or acorn squash, keeping in mind they have a creamier, less noodle-like flesh.
Is this recipe gluten-free?
Absolutely! This Chicken Fajita Spaghetti Squash Bowls Recipe is naturally gluten-free as long as your salsa and seasonings are verified gluten-free, making it perfect for those with gluten sensitivities.
How spicy is this recipe?
The spice level is moderate, thanks to the combination of chili powder and cayenne pepper. You can adjust the cayenne amount to your preference or omit it completely if you want a milder dish.
Can I substitute the chicken with another protein?
Definitely! This fajita mixture works wonderfully with shrimp, beef strips, or even tofu to suit your dietary preferences or what you have on hand.
What’s the best way to reheat leftovers without drying out the chicken?
Reheat gently over low to medium heat on the stovetop with a splash of water or salsa to keep the chicken moist. Microwaving with a cover can also help retain moisture but stir occasionally for even warming.
Final Thoughts
This Chicken Fajita Spaghetti Squash Bowls Recipe is one of those dishes that feels like a warm hug on a plate and delivers on flavor, nutrition, and fun presentation. It’s perfect for weeknight dinners or impressing guests with minimal fuss. Give it a try—you might just find yourself making it again and again because once you taste those savory fajita fillings nestled in tender squash, there’s no going back!
Print
Chicken Fajita Spaghetti Squash Bowls Recipe
- Prep Time: 15 minutes
- Cook Time: 1 hour
- Total Time: 1 hour 15 minutes
- Yield: 6 servings
- Category: Main Course
- Method: Baking
- Cuisine: Mexican-American Fusion
Description
Chicken Fajita Spaghetti Squash Bowls are a vibrant, healthy twist on traditional fajitas, combining roasted spaghetti squash with seasoned chicken, sautéed peppers and onions, and melted cheddar cheese. This recipe is perfect for a flavorful, low-carb meal that seamlessly blends Mexican-inspired spices with nutritious ingredients for a satisfying dinner.
Ingredients
Spaghetti Squash
- 1 spaghetti squash (cut in half length-wise, seeds removed)
- 2 tablespoons olive oil (divided)
- Salt and pepper to taste
Chicken and 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
- â…› teaspoon cayenne pepper
- 3 tablespoons olive oil
- 2 tablespoons lime juice
Vegetables
- 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
Additional Ingredients
- ¾ cup salsa (+ extra for topping)
- 1 ½ cups cheddar cheese (divided into ¾ cup portions)
- Green onions (optional, for serving)
Instructions
- Preheat the Oven: Preheat your oven to 425°F (220°C) to prepare for roasting the spaghetti squash.
- Prepare Spaghetti Squash: Drizzle 1 tablespoon olive oil on the inside of each spaghetti squash half, sprinkle with salt and pepper, and rub it evenly over the flesh. Place the halves cut-side down on an aluminum foil-lined baking sheet.
- Roast Squash: Bake the spaghetti squash in the preheated oven for 50 minutes, or until the flesh is tender and can be shredded with a fork.
- Mix Seasonings for Chicken: In a small bowl, combine cumin, chili powder, onion powder, garlic powder, salt, pepper, and cayenne pepper. Stir well to blend the spices evenly.
- Prepare Chicken Marinade: Add 3 tablespoons olive oil and 2 tablespoons lime juice to the seasoning mix and stir to combine.
- Marinate Chicken: Place cubed chicken into a gallon Ziploc bag. Pour in the marinade, seal, and toss to coat the chicken evenly. Refrigerate until ready to cook.
- Sauté Vegetables: With about 25 minutes left on the squash roasting time, heat 2-3 tablespoons olive oil in a skillet over medium heat. Add sliced bell peppers, onion, crushed garlic, salt, and pepper. Sauté, stirring constantly, for 16-18 minutes until vegetables are caramelized and golden brown.
- Cook Chicken: When there are about 15 minutes left on the squash timer, heat another skillet to medium heat. Add the marinated chicken cubes, avoiding too much marinade excess, and cook for about 10 minutes until thoroughly cooked. Drain any liquid as the chicken cooks.
- Combine Chicken and Vegetables: Add the cooked chicken to the skillet with the sautéed vegetables. Stir in salsa and ¾ cup cheddar cheese. Mix well until the cheese is melted and evenly distributed.
- Fill Squash Bowls: Remove the roasted spaghetti squash from the oven. Using a fork, fluff the squash strands lightly. Divide the chicken fajita mixture evenly into each squash half. If needed, gently remove some squash flesh to fit all filling.
- Add Topping and Bake: Sprinkle the remaining ¾ cup cheddar cheese over the filled squash halves. Return to the oven and bake for an additional 5 minutes at 425°F, until the cheese is golden and bubbly.
- Serve: Remove from oven, garnish with chopped green onions and extra salsa if desired. Serve warm and enjoy your flavorful, healthy Chicken Fajita Spaghetti Squash Bowls!
Notes
- You can use a gluten-free taco seasoning packet instead of the individual spices if preferred.
- To make fitting all the filling easier, carefully shave off some cooked spaghetti squash flesh as needed.
- Caramelizing the vegetables well enhances their natural sweetness and adds depth of flavor.
- If you want more heat, increase the cayenne pepper slightly or add chopped jalapeños with the bell peppers.
- This dish is great for meal prepping; store leftovers in airtight containers and reheat gently before serving.
- For a lower fat version, reduce the cheese quantity or use a low-fat cheese variety.

