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Home Recipes by Type Main Dish
GF Gluten-Free

Chicken Fajita Stuffed Spaghetti Squash

4.75
/5
55 mins
8 Comments
Jump to Recipe Video
By: Rachel GurkPosted: 01/06/2021Updated: 03/07/2022

This post may contain affiliate links. Please read my disclosure policy.

Colorfully topped spaghetti squash half, text overlay reads "chicken fajita stuffed spaghetti squash, rachelcooks.com"
Colorfully topped spaghetti squash half, text overlay reads "chicken fajita stuffed spaghetti squash, rachelcooks.com"
Colorfully topped spaghetti squash half, text overlay reads "chicken fajita stuffed spaghetti squash, rachelcooks.com"
Colorfully topped spaghetti squash half, text overlay reads "chicken fajita stuffed spaghetti squash, rachelcooks.com"

All the fixings of fajitas are deliciously combined in chicken fajita stuffed spaghetti squash for a filling and healthy main dish.

Recipe Overview

Why you’ll love it: It’s healthy, fun, and delicious!

How long it takes: 55 minutes
Equipment you’ll need: baking pan, oven, large skillet
Servings: 2 large servings

Overhead view of a spaghetti squash half, stuffed with chicken, bell peppers, and topped with fajita toppings.
Table of Contents
open
  • 1 Recipe Overview
  • 2 About This Recipe
  • 3 What You’ll Need
  • 4 Don’t have cooked chicken?
  • 5 How To Make This Recipe
  • 6 FAQs
  • 7 Make It Your Own
  • 8 Storage & Reheating Tips
  • 9 Stuff it!
  • 10 Get the Recipe: Chicken Fajita Stuffed Spaghetti Squash

Tender shredded chicken, with seared sweet red onion and colorful bell pepper strips, seasoned perfectly, all piled into a spaghetti squash bowl, and topped with a flavorful Mexican cheese blend, melty and warm. Are you on board yet? I know I am! If you are a fajita fan, you’ll love this lower calorie, low carb version.

Have you tried spaghetti squash yet? These oval yellow wonders are really kind of amazing. Cut one in half, bake it cut side down, flip it over, and use a fork to loosen the magical strands of “spaghetti” that appear. If you haven’t tried cooking spaghetti squash yet, I have a handy how-to prepare spaghetti squash tutorial that makes it easy. Truly, the hardest part is cutting those babies in half! 

Our love affair with spaghetti squash started with simple spaghetti squash with Parmesan and herbs that can be served just as it is for a delicious and unique side dish, or it can be topped with spaghetti sauce, vegan bolognese, marinara, or another sauce of your choice, for a delicious entrée. Next came pizza stuffed spaghetti squash, and who doesn’t like pizza?

Still wavering? My mom serves stuffed spaghetti squash almost weekly and my dad, a professed squash hater, chows it down every time! Give it a try and I bet you’ll soon find it in your weekly rotation!

Two halves of a spaghetti squash, topping with fajita toppings.

About This Recipe

Basically, once you get the squash baked, you just pile the fajita toppings into the squash bowl (shell), sprinkle cheese on top and broil until the cheese is melted. So easy! 

Like any fajita, it’s easy to customize each spaghetti squash half so everyone is happy. You can be creative with fresh toppings that are added, too. Keep reading for topping ideas.

I’ll get you started on the recipe here and give you extra tips to help out.

Look for the printable recipe card near the end of the post with complete instructions, measurements, and nutrition information.

Close up of a spaghetti squash half stuffed with chicken fajita ingredients.

What You’ll Need

  • Spaghetti Squash: Any size will work, but keep in mind that larger squashes take longer to cook and may be too much for two servings.
  • Cooked Chicken: I usually use boneless skinless chicken breasts but any type of cooked chicken is fine, including rotisserie chicken or canned chicken. It’s economical to buy a large package of chicken and either cook it in your Instant Pot or poach it on the stove. Store it in the refrigerator or freezer and you’ll have a head start on lots of good meals.
  • Red Onion: Yellow onions or sweet onions will also work in a pinch.
  • Bell Peppers: A variety of colors will make your spaghetti squash extra pretty, but really any color will work.
  • Fajita Seasoning: Make your own with this easy recipe or buy store-bought.
  • Shredded Cheese: We like to use a Mexican blend, but cheddar, pepper jack, and Monterey jack all work well here.
  • Toppings: Sour cream, salsa, guacamole, salsa verde, chopped tomatoes, cilantro, sliced jalapeño peppers, whatever you like!

Don’t have cooked chicken?

You might like this alternative to sautéing the chicken, peppers, and onions on the stove. I often make sheet pan fajitas. Simply toss everything on a sheet pan and put it in the oven right along with the sheet pan containing the squash. The squash will take 45-50 minutes to bake, the fajita ingredients about 15 minutes, so you can get the squash started first and then prepare the other sheet pan and bake it for the last fifteen minutes. Easy peasy.

How To Make This Recipe

You’ll need a little less than an hour to have dinner on the table.

The first step is getting the spaghetti squash into the oven to roast. Scrub the squash well and cut it in half vertically, from the stem end to the blossom end. Use a large sharp knife and a sturdy cutting board, and be careful! They can be a little hard to cut.

Once you have it cut in half, use a metal spoon to scrape out the seeds. They can be discarded or put into a compost bin. Rub a little olive oil on the cut surfaces and sprinkle a little salt and pepper on each half.

Line a baking pan with parchment paper for easy clean up. Place the halves cut side down in the pan. Bake the squash thirty-five to forty minutes or until it’s tender.

While the squash is baking, you’ll have plenty of time to get the fajita toppings ready. Slice the onion and peppers and put them in a large skillet with a bit of olive oil. Sauté them until they soften, then add the cooked chicken and fajita seasoning. Stir and cook until everything is warm and coated with seasoning. Looking good, right?

Once the squash is roasted to perfection, take it out of the oven, flip each half over and loosen the shreds of squash. A fork works perfectly. Just pull the squash strands away from the sides and make sort of a nest for the fajita fixings.

Sprinkle on a little cheese and pop the pan under the broiler for a minute or two, just to melt the cheese. Doesn’t that look good enough to eat?!

Add any fresh toppings that you like and dig in!

You won’t need to serve anything alongside this dish. It’s pretty much an all-in-one meal, satisfying and filling (and less than 500 calories!).

Close up of a chicken fajita stuffed spaghetti squash with toppings.

FAQs

Is spaghetti squash healthy?

Yes! It’s low in calories and carbohydrates but it’s high in nutrients and fiber. Spaghetti squash is a winter squash and is loaded with antioxidants like beta-carotene and vitamin C (Healthline).

Does spaghetti squash taste like pasta?

Sorry, it doesn’t really taste like pasta. The “spaghetti” name refers more to the fibrous strands that look somewhat like pasta. Spaghetti squash has almost a nutty flavor, sort of buttery and a little sweet. It’s rather neutral in flavor so it goes wonderfully with most sauces and toppings, much like pasta.

Is spaghetti squash called anything else?

You may know it as noodle squash, vegetable squash, vegetable spaghetti, or vegetable marrow (Cucurbita pepo).

Make It Your Own

  • Make vegetarian fajita stuffed spaghetti squash by simply omitting the chicken and substituting black or pinto beans.
  • Prefer a steak fajita? Sauté thinly sliced steak of your choice and add to the peppers and onions. You could do the same with shrimp.
  • Make taco spaghetti squash! Use your favorite taco meat instead of the chicken. Add your favorite taco toppings, and lots of cheese.
A fork stuck in a spaghetti squash that has been filled with chicken fajita toppings.

Storage & Reheating Tips

While this dinner is truly best eaten right away, leftovers can be stored in the fridge for a day or two.

For best results, scrape everything out of the squash shell and put it in an airtight container. Reheat gently in the microwave.

Stuff it!

Now that you know how great stuffed spaghetti squash can be, try one of these stuffed yummies:

  • Vegetarian Stuffed Peppers
  • Stuffed Acorn Squash with Sausage and Apples
  • Chicken Parmesan Stuffed Portobello Mushrooms
  • Coq Au Vin Stuffed Mushrooms
  • Stuffed Pepper Casserole
  • Pesto and Cheese Stuffed Zucchini
  • Pepperoni Pizza Quinoa Stuffed Peppers
  • Quinoa, Kale and Bacon Stuffed Butternut Squash
  • Apple Gouda Stuffed Chicken Breasts with Smoky Roasted Sweet Potatoes — make it on a sheet pan!

Did you make this? Be sure to leave a review below and tag me @rachelcooksblog on Facebook, Instagram, or Pinterest!

Spaghetti squash full of bell peppers, onions, chicken and cheese. It is topped with sour cream, jalapeno, tomato, and sour cream.
Recipe

Get the Recipe: Chicken Fajita Stuffed Spaghetti Squash

4.75 from 4 votes
Prep Time: 10 mins
Cook Time: 45 mins
Total Time: 55 mins
2 large servings
Print Rate Recipe
Prevent your screen from going dark
All the fixings of fajitas are deliciously combined in chicken fajita stuffed spaghetti squash for a filling and healthy main dish.

Ingredients

  • 1 spaghetti squash, medium sized, scrubbed
  • 1 tablespoon olive oil, plus 1 teaspoon, divided
  • ¼ teaspoon salt
  • ⅛ teaspoon pepper
  • ½ red bell pepper, thinly sliced
  • ½ green bell pepper, thinly sliced
  • ½ red onion, sliced vertically into thin strips
  • 1 ½ cups cooked chicken, shredded
  • 1 tablespoon fajita seasoning
  • ½ cup shredded Mexican blend cheese
  • Toppings: Sour cream, chopped tomatoes, sliced jalapeño pepper, salsa, etc.

Instructions

  • Preheat oven to 400ºF. Line baking sheet with parchment paper.
  • Cut spaghetti squash in half lengthwise, from stem to bottom. Scoop out seeds. Rub spaghetti squash halves with one teaspoon olive oil, and sprinkle with salt and pepper. Place cut side down on prepared baking sheet. Bake 35-40 minutes or until fork tender.  
  • While squash is baking, heat a large skillet over medium high heat. Add one tablespoon olive oil, peppers, and onions. Sauté 7-8 minutes or until soft. Add chicken and fajita seasoning, cook and stir until chicken is heated through and everything is coated with seasoning, 1-2 minutes. Remove from heat.
  • Remove spaghetti squash halves from oven. Turn oven to broil setting. 
  • Lightly fluff strands with fork, so that they resemble spaghetti. 
  • Divide and add vegetables and chicken to the squash halves, mixing lightly with the squash strands. Sprinkle evenly with cheese.
  • Broil squash halves 4-5 minutes, or until cheese is bubbling and lightly browned. 
  • Remove from oven and top with desired toppings.

Notes

  • For 4 servings: Use 2 spaghetti squash and double the rest of the ingredients.
  • If preferred, stuff the squash with sheet pan fajitas. By using this method, you can make the fajita toppings, including raw chicken, in the oven while the squash bakes.
  • Vegetarian? Simply replace the chicken with black or pinto beans.
  • Prefer a steak fajita? Sauté thinly sliced steak of your choice and add to the peppers and onions. You could do the same with shrimp.
  • Make taco spaghetti squash! Use your favorite taco meat instead of the chicken. Add your favorite taco toppings, and lots of cheese.

Nutrition Information

Calories: 448kcal, Carbohydrates: 41g, Protein: 35g, Fat: 18g, Saturated Fat: 5g, Polyunsaturated Fat: 3g, Monounsaturated Fat: 8g, Trans Fat: 1g, Cholesterol: 89mg, Sodium: 825mg, Potassium: 1120mg, Fiber: 9g, Sugar: 17g, Vitamin A: 1937IU, Vitamin C: 76mg, Calcium: 450mg, Iron: 2mg

This website provides approximate nutrition information for convenience and as a courtesy only. Nutrition data is gathered primarily from the USDA Food Composition Database, whenever available, or otherwise other online calculators.

© Author: Rachel Gurk

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  1. Laurie says

    January 3, 2023 at 2:23 am

    5 stars
    This cooking method is very special. How would it taste if yogurt was used instead of cheese?

    Reply
    • Rachel Gurk says

      January 3, 2023 at 10:34 am

      That could be tasty! You’d want to use a full-fat plain yogurt. Lower fat percentages could curdle when you cook the squash.

      Reply
  2. Dacey says

    November 11, 2021 at 7:13 pm

    Once I scrape the insides out of the squash do I return those at the end after the squash bakes?

    Reply
    • Rachel Gurk says

      November 13, 2021 at 8:39 am

      The seeds stay out (assuming you’re not talking about those, but juuuust in case!). The squash itself you don’t take out, you just fluff up the strands with a fork and leave them right inside the squash. Hope that helps!

      Reply
  3. denise says

    January 6, 2021 at 11:57 pm

    such a creative idea

    Reply
    • Rachel Gurk says

      January 8, 2021 at 9:23 am

      Thanks Denise!

      Reply
  4. Linda says

    January 6, 2021 at 10:08 am

    Can the spaghetti squash be cooked in an Instant Pot? If yes, can you stack the two halves or would you need to do the independently? I’d like to keep cleanup to just the IPot and toss the foil I used for broiling.

    Reply
    • Rachel Gurk says

      January 8, 2021 at 9:28 am

      I have a post on how to cook spaghetti squash in an instant pot, but it’s not my preferred method since the squash gets a lot softer and a little watery. You could cook it in the oven on foil and use the same foil to broil it (that’s what I do). Then there are zero pans to clean!

      Reply

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