Fajita Spaghetti Squash Bake (2024)

This post may contain affiliate links. Please read mydisclosure policy.

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.

Fajita Spaghetti Squash Bake (1)

Fajita Spaghetti Squash Bake

Fall 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 fajitabut more nutrient-dense and hearty! It’s theis the ultimate gluten-free casserole lightened up!

Fajita Spaghetti Squash Bake (2)

Ingredients Needed

  • Spaghetti Squash
  • Chicken Breasts
  • Red Bell Pepper
  • Onion
  • Spices
  • Lime Juice
  • Pinto Beans
  • Cheddar Cheese

Want to make it vegetarian? Simply omit the chicken! Want tomake it paleo-friendly? Omit the beans and cheese!

Fajita Spaghetti Squash Bake (3)

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. To do that:

  1. Roast the spaghetti squash (or cook in an Instant Pot) following thisrecipe for cooking Spaghetti Squash.
  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.
Fajita Spaghetti Squash Bake (4)

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 store it as a side salad.

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. You can discard it before heating it up if it bothers you.

Fajita Spaghetti Squash Bake (5)

Watch the video here:

If you like this spaghetti squash recipe, check out these others:

  • Spinach and Artichoke Spaghetti Squash
  • How to Cook Spaghetti Squash
  • Chicken Enchilada Spaghetti Squash Casserole
  • Spaghetti Squash Pad Thai

Pin this recipe to save it for later!

Fajita Spaghetti Squash Bake (6)

FAJITA SPAGHETTI SQUASH BAKE

4.75 from 4 votes

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.

Servings 4

Prep Time 10 minutes minutes

Cook Time 1 hour hour

Total Time 1 hour hour 10 minutes minutes

Rate RecipePrint Recipe

Ingredients

  • 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

Instructions

  • Cook spaghetti squash using

    these

    directions.

  • 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.

  • Add back in chicken and remainder of ingredients and cook for 2 minutes.

  • 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.

  • Preheat broiler to high.

  • 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.

  • Place under the broiler until the cheese and melted and the mixture is completely heated through.

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.

Course: Dinner

Author: Lexi

Did you make this recipe?

Share a photo and tag @lexiscleankitchen — we can’t wait to see what you’ve made!

Fajita Spaghetti Squash Bake (2024)
Top Articles
Latest Posts
Recommended Articles
Article information

Author: Kelle Weber

Last Updated:

Views: 6315

Rating: 4.2 / 5 (53 voted)

Reviews: 92% of readers found this page helpful

Author information

Name: Kelle Weber

Birthday: 2000-08-05

Address: 6796 Juan Square, Markfort, MN 58988

Phone: +8215934114615

Job: Hospitality Director

Hobby: tabletop games, Foreign language learning, Leather crafting, Horseback riding, Swimming, Knapping, Handball

Introduction: My name is Kelle Weber, I am a magnificent, enchanting, fair, joyous, light, determined, joyous person who loves writing and wants to share my knowledge and understanding with you.