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Health and Wellness.

04 Feb

Healthy Fajita Spaghetti Squash Bake

By: Sandie Flynn Buller

Winter is the perfect time for spaghetti squash! Spaghetti Squash is a healthier alternative to pasta and it works so well here to lighten up this Fajita casserole recipe. With chicken, peppers, onions, beans, squash, and just the right amount of spice it’s like a classic fajita but more nutrient-dense and hearty! It’s the is the ultimate gluten-free casserole lightened up!

How to Make a Spaghetti Squash Bake

There are two ways to make this bake. Either as a casserole or as spaghetti squash boats!  You can either bake this as a casserole in an 8″x 8″ dish (or something similar) or you can bake directly inside the spaghetti squash halves – that’s what we do at my house to make it funner for the kids! To do that:

  1. Remove seeds and then roast the spaghetti squash in the oven (or cook in an Instant Pot) till done (can insert fork easily into).
  2. Meanwhile, make the fajita mixture.
  3. Once cooked and cooled, scoop out the spaghetti squash strands and combine with the fajita mixture.
  4. Place back in the empty shells of the spaghetti squash or place it in a baking dish and top with shredded cheese, if using.
  5. Place under the broiler until the cheese and melted and the mixture is completely heated through.

How to Serve and Store It

What makes a casserole or a bake so amazing is that it’s a meal all in one. It’s meant to be served as is! If you’d like, you could also freeze it and use later as a quick week night meal.

This will make a great meal prep lunch for a few days. To store, let it cool completely before setting aside portions in meal prep containers. This will last about 3 days in the refrigerator. The squash can give release some liquid as it sits or if it is frozen. You can discard the extra liquid before or after heating it up if it bothers you.


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 (optional) meal is the ultimate family casserole that is great for weekly meal prep, too.

Yield 4
Prep Time 10 minutes
Cook Time 1 hour
Total Time 1 hour 10 minutes


  • 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 in oven or instant pot with seeds removed.
  2. Meanwhile, make fajita mixture: Heat oil in a large pan over medium heat. Cook chicken until fully cooked, about 5 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.


  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 like using under your homemade spaghetti sauce!
  3. Want to make it vegetarian? Simply omit the chicken! Want to make it paleo-friendly? Omit the beans and cheese!

Hope you and your family enjoy these as much as me and mine!

To Your Good Health! Eat Well! Live Well!

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