When the Mexican food craving hits, this healthy Chicken Fajita Stuffed Spaghetti Squash is the perfect go-to dish! Spiced chicken is sautéed with colorful veggies and served in an oven roasted squash bowl as a low carb alternative.
A Healthy Mexican Recipe
As any reader would know, I love Mexican food. The issue is, it's not always the most waistline friendly food around (at least not at my house).
This satisfying healthy chicken fajita stuffed spaghetti squash is my go-to meal when I'm craving some delicious but guilt-free Mexican food.
Summer is just around the corner, so I figure it's time for me to start incorporating some lower carb meals into my life. When I’m on a clean eating plan, I always look for delicious keto chicken recipes or a Paleo chicken recipe or anything under the Whole30 diet.
How to prepare spaghetti squash
The "tortilla" of this fajita is a beautifully roasted spaghetti squash half. The squash can be cooked in either the oven or microwave. I prefer the taste of a roasted, oven-baked squash, but if you don't have the time, the steamed microwave version works just fine.
However you choose to cook it, spaghetti squash oven or spaghetti squash microwave, it gives this dish some great texture and makes it a more substantial entree.
Make a homemade taco seasoning mix for the stuffed spaghetti squash
Obviously, I'm a big fan of beef when it comes to tacos (like these crockpot shredded beef tacos and these Instant Pot beef tacos), but I love Mexican recipes with chicken too! I also love healthy spaghetti squash recipes that combine bold and bright flavors and that's what this recipe is all about.
How to make a healthy chicken fajita marinade? By using a homemade chicken fajita seasoning!
It's simply not worth it to buy a premade fajita marinade or taco seasoning mix when you can make your own that tastes better and costs a whole lot less.
PIN it for later to make this healthy Chicken Fajita Stuffed Spaghetti Squash the next time you've got a hankering for some south of the border tastes!
Recipe

Chicken Fajita Stuffed Spaghetti Squash
Ingredients
- 2 spaghetti squashes , cut in half lengthwise and seeds removed (about 3 pounds each)
- 3 chicken breasts , skinless and boneless , cut into 1 ½ inch pieces
- 2 tablespoons chili powder
- 2 teaspoons dried oregano
- 2 teaspoons garlic powder
- 1 teaspoon ground cumin
- ¼ teaspoon ground cinnamon
- 1 lime , zested and juiced
- 2 medium sized bell peppers , cut into thin slices (red, green, and/or yellow)
- 2 medium sized onions , cut into thin slices
- 3 tablespoons cooking oil , separated
- sea salt and fresh ground black pepper , to taste
- 1 ½ cups Monterey Jack or Pepper Jack cheese , shredded
- optional accompaniments: sour cream , guacamole , chopped cilantro , lime slices,
- and pico de gallo
Instructions
- Preheat oven to 400F degrees. Coat with the inside of each squash with 1 tablespoon of oil and season lightly with salt and pepper. Place the four squash halves flesh side down on a baking sheet. Bake for 50 minutes, or until the squash is fork tender.
- While the squash is baking, prepare the chicken. In a large bowl, combine the chili powder, oregano, garlic powder, cumin, cinnamon, lime zest and juice. Add the chicken pieces and mix until thoroughly coated. Cover the bowl and place in the refrigerator until ready to use.
- About 10 minutes before squash is finished cooking, heat 1 tablespoon of oil in a large pan over medium-high heat. Add the bell peppers and onion slices and saute until tender-crisp (about 5-6 minutes). Remove from pan and set aside.
In the same pan, add the remaining 1 tablespoon of oil and saute the chicken pieces over medium-high heat for 3-5 minutes. Add the pepper and onion mixture back to the pan, mix together with the chicken, and saute for another minute. Add salt and pepper to taste. - When the spaghetti squash is finished cooking, remove from oven and increase temperature to 425F degrees. Turn each squash half flesh side up and fill each half with an equal amount of the chicken fajita mixture. Top with the shredded cheese and place back in the oven for 5 minutes, or until the cheese is melted.
Trudi
I added black beans, corn a n enchilada sauce and it was exceptional. The whole family loved it
Karrie
Very happy everyone loved it Trudi and thank you so much!
Thao @ In Good Flavor
My daughter would love this (I do too!) because she is trying to stick to a mostly clean diet. I love the roasted squash bowl! I'll have to make this for her the next time we have a girl's lunch or dinner!
Karrie
Clean is the way to go Thao!
Katie Crenshaw | A Fork's Tale
Karrie, these look great! I am glad you made these. I need some healthy tasty recipes while I am trying to loose those darn unwanted pounds. This is perfect.
Karrie
Thank you Katie!
Diego Lopes
This looks so good! I saw a similar recipe that was stuffed avocado, also looked pretty good. Can't wait to try it!
Karrie
Thanks Diego!
Milena | Craft Beering
That's a fun take on spaghetti squash! And I can never say 'no' to chicken fajitas, so I guess this recipe is happening:)
Dawn - Girl Heart Food
I have two spaghetti squash in my pantry all ready to use! I'm doing a whole meatless March thing, but would love to try these in April. They look SO good, especially with all that cheese on top Way to mix up taco Tuesday! Pinned! P.S. Love your pics!
Karrie
Thank you and agreed that this is awesome for Taco Tuesday!