Chicken Fajita Stuffed Spaghetti Squash

At a glance

What stands out: All the fixings of fajitas are deliciously combined in chicken fajita stuffed spaghetti squash for a filling and lighter main dish. It’s straightforward and rich!

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

Fajita Stuffed Spaghetti Squash

Tender shredded chicken, with seared sweet red onion and colorful bell pepper strips, seasoned evenly, all piled into a spaghetti squash bowl, and topped with a flavorful Mexican cheese blend, melty and warm. Are you on board yet? We know we are! 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 kind of memorable. 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, we have a handy how-to prepare spaghetti squash tutorial that makes it straightforward. 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 rich and unique side dish, or it can be topped with spaghetti sauce, vegan bolognese, marinara, or another sauce of your choice, for a rich entrée.

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

About This Fajita Recipe

A straightforward way to serve fajitas. Basically, once you get the squashes baked, you just pile the fajita toppings into the squash bowls (shell), sprinkle cheese on top and broil until the cheese is melted. So straightforward!

Lots of ways to customize. Like any fajita, it’s straightforward to prepare each spaghetti squash half just the way each person likes it. If you have someone in your family that’s a vegetarian, they can skip the chicken. Another person may need to omit the cheese. Our dad doesn’t like peppers, so we make one squash half without. You can be creative with fresh toppings that are added, too. Keep reading for topping ideas.

What goes in

• Spaghetti Squash: Any size will work, but keep in mind that larger squashes take longer to cook and may be too much for four servings. We like to buy 2 smaller-sized squashes so everyone gets their own squash half to fill.
• Cooked Chicken: We 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 any color will work.
• Fajita Seasoning: Make your own with this straightforward 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. We 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. Straightforward peasy.

How it comes together

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

Prep and bake the squash. 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 straightforward clean up. Place the halves cut side down in the pan. Bake the squash thirty-five to forty minutes or until it’s tender.

Sauté the peppers and onions. 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?

Loosen the squash strands. 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 evenly. Just pull the squash strands away from the sides and make sort of a nest for the fajita fixings.

Stuff the squash and broil. Add the chicken and vegetables that you sautéed. 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?!

Serve. 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!).

Before you start

Ways to change it

• Vegetarian: Omit the chicken and substitute black or pinto beans.
• Steak or shrimp fajita: Sauté thinly sliced steak of your choice and add to the peppers and onions. You could do the same with shrimp.
• Taco spaghetti squash: Use your favorite taco meat instead of the chicken. Add your favorite taco toppings, and lots of cheese.
• Pizza stuffed spaghetti squash: We love this recipe! Add a little pizza sauce to each squash half, lots of mozzarella cheese, and your favorite pizza toppings. Straightforward and rich!

Keeping leftovers

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.

Free Meal Plan

Interested in a weekly meal plan that includes this recipe? Take a look at Meal Plan #81. You’ll find a wholesome recipe for each weekday plus a categorized grocery list. We add a new meal plan weekly.

Browse Meal Plans

• Yield: 4 servings
• Prep: 10 minutes
• Cook: 45 minutes
• Total: 55 minutes

Ingredients

• 2 small spaghetti squash (1 ½ pounds each), scrubbed
• 2 tablespoons olive oil, plus 2 teaspoons, divided
• ½ teaspoon salt
• ¼ teaspoon pepper
• 1 red bell pepper, thinly sliced
• 1 green bell pepper, thinly sliced
• 1 red onion, sliced vertically into thin strips
• 3 cups cooked chicken, shredded
• 2 tablespoons fajita seasoning
• 1 cup shredded Mexican blend cheese
• Toppings: Sour cream, chopped tomatoes, sliced jalapeño pepper, salsa, etc.

Method

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

Notes

Shortcut: 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.

Steak/shrimp variation: Sauté thinly sliced steak of your choice and add to the peppers and onions. You could do the same with shrimp.

Taco spaghetti squash: Use your favorite taco meat instead of the chicken. Add your favorite taco toppings, and lots of cheese.