Fajita Spaghetti Squash Bake

This Fajita Spaghetti Squash Bake is comfort food lightened up! All the classic flavors of enchiladas, but made healthier and more nutrient-dense with spaghetti squash as its base. This gluten-free and dairy-free meal is the ultimate family casserole that is great for meal prep, too.

Prep Time 10 minutes
Yield 4
Cook Time 1 hour
Recipe Type: Dinner
Difficulty: Easy
Total Time 1 hour 10 minutes
Author: [get-the-author]


  • 1 (2 pound) spaghetti squash (see note)
  • 2 teaspoons oil
  • ½ pound boneless, skinless chicken breasts, sliced into ½” strips (omit for vegetarian)
  • 1 red bell pepper, cored and sliced in ½” strips
  • 1 small onion, sliced
  • 1 teaspoons chili powder
  • 1-1/2 teaspoon fine sea salt
  • ½ teaspoon ground black pepper
  • ½ teaspoon smoked paprika 
  • ½ teaspoon cumin
  • 2 tablespoons lime juice (from 1 lime)
  • 1 cup canned pinto beans, drained and rinsed 
  • ½ cup cheddar cheese


  1. Cook spaghetti squash using these directions.
  2. Meanwhile, make fajita mixture: Heat oil in a large pan over medium heat. Cook chicken until fully cooked, about 4 minutes on each side. Remove. Add in a splash more oil if the pan is dry, and add in onions and peppers and cook until beginning to soften, about 5 minutes. 
  3. Add back in chicken and remainder of ingredients and cook for 2 minutes.
  4. Once spaghetti squash is cooked and cooled enough to handle, scoop out the squash into a large bowl. Add in beans and ¼ cup cheddar cheese (if using), and fajita mixture. Mix together gently until fully combined.
  5. Preheat broiler to high.
  6. Either divide the mixture into the now empty squash shells and top with remaining cheese or place in an 8" x 8" oven safe casserole dish.
  7. Place under the broiler until the cheese and melted and the mixture is completely heated through.

Recipe Notes

  1. The fajita mixture will taste spicy before adding it together with the cooked squash.
  2. This mixture is based on spaghetti squash that is around 2 pounds. If your spaghetti squash is larger than that just use 4 heaping cups of cooked spaghetti squash, and set aside the rest for other use.


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