Chicken Fajita Casserole (Healthy!)

Published by:
Liz Marino
| 07/19/2021 | Last Updated: 10/14/2025

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This easy Chicken Fajita Casserole Recipe is made in one pan with only a few ingredients. Secretly healthy, quick to make and delicious!

An overhead image of chicken fajita casserole on a white dish on a grey background with other dishes and casserole off to the side.


 

If you’re looking for a yummy casserole that’s easy to make in one pot, and has all the delicious flavors of chicken fajitas – look no further!

This Chicken Fajita Casserole is a staple in our weeknight dinner rotation, and I know you’re going to love it!

Everything is cooked in one dish, which means fewer dishes and less clean-up, but it packs in 40g of protein in each serving, so it’s both satisfying and nutritious.

We also love these crock pot chicken fajitas and Mexican Chicken Casserole for something just as tasty and easy to make!

Liz’s top tips for fajita casserole

  • Use an oven-safe pan: This recipe starts cooking on the stovetop and ends in the oven, so to keep it a one pan recipe, use a pan that is safe for both cooking methods.
  • Customize your spice level: If you don’t like spice, omit the jalapeno; conversely, if you really like a spicy dinner, add a little extra!

Ingredients

Ingredients for Chicken Fajita Casserole in small white bowls on a grey background

Substitutions

Rice: You can find frozen brown rice in the freezer section at most grocery stores. I usually get mine from Walmart or Trader Joe’s. Do not use dry rice products. Do not use white rice. The brown rice holds texture. Frozen rice works best here, but you can also use the 90 second bags of rice in the dry goods aisle if you can’t find them. Just don’t cook them first. Take them straight from the bag and add them to the pan. We haven’t tried quinoa or any other grain in this recipe, so I don’t know how it will work.

Jalapeño – Jalapeño is optional; omit it for less spice.

Chicken Breasts– Chicken breasts can be substituted with chicken thighs or chicken tenders

Beans – Beans would make a great addition to this meal. Black beans or pinto beans would work best.

Taco Seasoning– I recommend using our homemade Taco Seasoning, it’s lower in salt. You can also use store bought taco seasoning.

Low salt – This can easily become a high sodium meal. We recommend omitting the salt if you’re using store bought homemade taco seasoning, as this will be much higher in salt. We used our homemade taco seasoning, which is much lower in salt.

Cheese – Mexican, cheddar, or pepper jack cheese all work in this recipe. You can also omit the cheese.

Garlic: If you don’t have fresh minced garlic, substitute with 1 teaspoon garlic powder.

Onion: If you don’t have fresh onion, substitute with 1 teaspoon onion powder.

How to make chicken fajita casserole

Chicken on a plate on a grey background on a white dish
  1. Spray a pan with olive oil and heat over medium high heat. Season with taco seasoning. When hot, brown the chicken on each side for about 2 minutes per side. Remove it and set it aside.
vegetables sautéing in a dutch oven for chicken fajitas casserole
  1. Add the onion, bell peppers, garlic, and jalapeño to the pan. Sauté for 2 minutes or until translucent.
brown rice, greek yogurt, vegetables and spices in a cast iron dutch oven
  1. Move the pan off the heat and add in the frozen brown rice, Greek yogurt, ¼ cup shredded cheese, 1/2 tablespoon taco seasoning, salt, and pepper. Stir together, then place the chicken breasts on top.
chicken fajita casserole in a cast iron dutch oven before being baked in the oven
  1. Cover with foil and bake at 400 degrees for 25-27 minutes or until the chicken is 165° in the center.
A close up of easy chicken fajita casserole fresh out of the oven
  1. Remove the foil and add the remaining ¼ cup of shredded cheese. Turn the oven to broil and broil until the cheese is melted and starting to crisp.

We love this instant-read thermometer for checking the internal temperature to make sure your meat is cooked thoroughly!

serving Suggestions

This Chicken Fajitas Casserole is great on its own. It’s a complete meal with protein, fat, and carbs.

We like to top this with guacamole or avocado, salsa (this Pineapple Mango Salsa or Corn Salsa is my favorite!), red onion, or fresh cilantro. You could also try sour cream, flour tortillas, or tortilla chips and enjoy with a Skinny Margarita or Cucumber Vodka Cocktail with Lemonade.

You can also make these Fajita Veggies if you’re looking to add more vegetables to your plate

Storage

Refrigerator: You can store this southwest casserole in the refrigerator for up to 4 days.

Freezing: You can freeze this casserole recipe, but we do not recommend it. We’ve found it can get a little mushy once thawed.

Reheating: This Chicken Fajita Casserole tastes great when reheated! You can reheat in the microwave, in the oven set at 350°F until the center is warmed through, or sauté on the stove.

It’s best to store this casserole in the refrigerator and enjoy it fresh.

A Chicken Fajita Casserole on a white dish with a fork taking a bite out of it.

Other healthy casserole recipes:

We love healthy casseroles! Here are some of our favorites:

An overhead image of chicken fajita casserole on a white dish on a grey background with other dishes and casserole off to the side.

Chicken Fajita Casserole

Recipe by: Liz Marino
5 from 13 votes
This easy Chicken Fajita Casserole Recipe is made in one pan with only a few ingredients. Secretly healthy, quick to make and delicious!
Prep Time : 10 minutes
Cook Time : 30 minutes
Total Time : 40 minutes
Serves : 4 people
(hover over # to adjust)

Ingredients

  • 1.5 lbs boneless, skinless chicken breasts (about 3-4 breasts depending on size ) pound to even thickness. Should be no more than 1.5 inches thick
  • 3 tablespoons taco seasoning divided 2.5 for chicken and ½ tbsp, for rice mixture
  • 1 cup bell pepper chopped
  • 1 cup onion chopped
  • 1/2 tablespoon jalapeño deseeded & minced- OPTIONAL
  • 3 teaspoon garlic minced
  • 1/2 teaspoon salt
  • ½ teaspoon black pepper
  • ½ cup nonfat greek yogurt
  • ½ cup Mexican blend cheese or cheddar, divided
  • 16 ounces frozen brown rice-uncooked

Instructions

  1. Note: You want to use a pan you can transfer to the oven (stainless steel, cast iron , or a cast iron enamel braising pot are all great. Do not use Teflon or anything with a plastic handle).
  2. Spray a pan with olive oil and heat over medium high heat. Season the outside of the chicken with 2 tablespoons of taco seasoning.
  3. When the pan is hot, brown the chicken on each side for about 2 minutes per side. When it’s brown on each side, remove it and set aside on a plate.
  4. Add in the onion, pepper, garlic, and jalapeño to the pan. Sauté for 2 minutes or until translucent.
  5. Move the pan off the heat and add in the frozen brown rice, Greek yogurt, ¼ cup cheese, 1 tablespoon taco seasoning, salt and pepper. Stir together then place the chicken breasts on top.
  6. Cover with foil and bake at 400 degrees for 25-27 minutes or until the chicken is 165 in the center.
  7. Remove the foil and add the remaining ¼ cup of cheese. Turn the oven to broil and broil until the cheese is melted and starting to crisp.
  8. Allow to cool for 5-10 minutes, garnish with fresh pico and avocado and serve.

Video

Nutrition Facts

Serving: 2cups chicken, rice, vegetables (estimated) | Calories: 411kcal | Carbohydrates: 36g | Protein: 46g | Fat: 8g | Saturated Fat: 3g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 2g | Trans Fat: 1g | Cholesterol: 119mg | Sodium: 592mg | Potassium: 921mg | Fiber: 4g | Sugar: 5g | Vitamin A: 1499IU | Vitamin C: 56mg | Calcium: 225mg | Iron: 2mg
Course: Main Course
Cuisine: Mexican
Tried this recipe?Share it! Make sure to tag @thecleaneatingcouple or use #thecleaneatingcouple!

Important Note: This is not an authentic Mexican recipe. My goal is always to share recipes that are a bit healthier and made with affordable, accessible ingredients so everyone can enjoy them regardless of their food allergies or dietary restrictions.

5 from 13 votes (1 rating without comment)

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Recipe Rating




35 Comments

  1. Julie McCarthy says:

    Can we simply omit the rice as I don’t typically eat rice. I would prefer to use some quinoa or cauliflower rice.

    1. I’m sorry, but I’ve only made this recipe with rice. Cauliflower rice will not absorb the broth, and definitely will not work. Quinoa might, but without trying it, I can’t be sure.

  2. 5 stars
    Quick and easy recipe with incredible flavors! I substituted cauliflower rice for the brown rice. Everyone loved it!

  3. 5 stars
    this was so simple to put together and yet tasted like i had spent hours preparing it. I doubled the chicken because of my 21 yr old son – I wanted to make sure I got some. Used dairy free Daiya cheese and 90 min brown rice. Topped with fresh salsa.

  4. Looks delicious! If a Dutch oven is used, should you use the Dutch oven lid instead of the aluminum foil?

  5. Stephanie Guardino says:

    5 stars
    This Recipe is so delicious! Highly recommend and made as is!

  6. I used left over cooked chicken, therefore didn’t need to bake.
    I also used 1 tblsp less of taco seasoning….still spicy enough for me (I’m a lightweight spice person).

    Very yummy!! We all loved it!!

  7. Recipe calls for 3 tablespoons of taco seasoning. It said to put 2 tablespoons on chicken and 1/2 tablespoon taco seasoning in with the yogurt mixture that goes into rice. Where does the other half tablespoon go? Is there a mistake in recipe?

    1. The Clean Eating Couple says:

      Sorry for the confusion there was a typo. 2 tablespoons goes on chicken, 1 tablespoon goes in the rice! Just updated it

  8. I’m not familiar with frozen brown rice. Is it already cooked? Could you use instant brown rice instead or regular brown rice.

    1. The Clean Eating Couple says:

      All of our blog posts have a green substitutions section. Pasting the info about the rice here: You can find frozen brown rice in the freezer section at most grocery stores. I usually get mine from Walmart or Trader Joe’s. Do not use dry rice products. Do not use white rice. The brown rice holds texture. Frozen rice works best here, but you can also use the 90 second bags of rice in the dry goods aisle if you can’t find them. Just don’t cook them first. Take them straight from the bag and add them to the pan. We haven’t tried quinoa or any other grain in this recipe so I don’t know how it will work.

  9. Hannah Garcia says:

    We have a dairy allergy in our home. I have a hard time finding a cheese for Mexican dishes. Mykonos works great for Italian dishes. Do you have anything you recommend to make this dairy free?

    1. The Clean Eating Couple says:

      I haven’t tried making this dairy free! If you’d like to try dairy free yogurt and cheese feel free and let me know how it comes out! or if you just skip the dairy I’m sure it would also be fine. good luck 🙂

    2. I use Daiya cheese- non dairy and love it! I use it in all recipes.

  10. 5 stars
    Love this recipe – made it over the summer and it was great! Could you do all the steps for this recipe except the baking a day ahead and bake the next day?

    1. The Clean Eating Couple says:

      I wouldn’t recommend it, think the rice would get a funny texture. You could maybe sear the chicken/saute the veggies ahead of time, but I think you’re better off to bake it and reheat it when ready to serve

  11. 5 stars
    Super tasty and easy to make! Used frozen bell pepper, onions and tossed in some frozen corn and black beans. Also, used the frozen rice medley from Trader Joe’s and it came out wonderful!

  12. 5 stars
    This was delicious!!! I couldn’t find frozen brown rice (only had time to check Aldi) but used a 90 second quinoa/brown rice mix like the substitutions suggested. It was so good! I can’t stand Greek yogurt and was a little nervous about using it, but happy to report I couldn’t taste it at all!! My husband was a huge fan, too. Adding it to our meal rotations- thank you!

  13. Ethel Sweed says:

    can I used chicken thighs instead of breasts? What brand of organic taco seasoning do you prefer?

  14. Ethel Sweed says:

    can I use quinoa instead of brown rice?

    1. The Clean Eating Couple says:

      Please read our substitution section.

      Rice Substitutions: You can find frozen brown rice in the freezer section at most grocery stores. I usually get mine from Walmart or Trader Joe’s. Do not use dry rice products. Do not use white rice. The brown rice holds texture. Frozen rice works best here, but you can also use the 90 second bags of rice in the dry goods aisle if you can’t find them. Just don’t cook them first. Take them straight from the bag and add them to the pan.

      Chicken Substitutions: Chicken breasts can be subbed with chicken thighs or chicken tenders

    2. Ethel Sweed says:

      can I use quinoa instead of brown rice?

      Ethel Sweed

      1. The Clean Eating Couple says:

        We haven’t tried quinoa or any other grain in this recipe so I don’t know how it will work.

  15. Shawna Camden says:

    5 stars
    This recipe was so easy, not too many ingredients and delicious! My husband, who does not like “healthy” food enjoyed it as well!

    1. The Clean Eating Couple says:

      So glad you liked it, Shawna! Thank you!

  16. Lyndi Zavy says:

    5 stars
    This was a HUGE hit for my family (2 kids 3 & 8 and my husband, all fairly picky!). It was super easy and so flavorful, we even fought over the leftovers the next day. This is definitely going into our weekly rotation!

    1. The Clean Eating Couple says:

      Thanks, Lyndi!!

  17. 5 stars
    We love this casserole! Can you substitute frozen cauliflower rice?

    1. The Clean Eating Couple says:

      I haven’t tried making it with frozen cauliflower rice but I think it would result in a mushy mess. If you are going to try it, I would use raw cauliflower rice instead of frozen because it will be less watery, but I honestly don’t think it will come out very good. If you try it let me know!

  18. Griff Neilson says:

    5 stars
    Wow, the brown rice really does give this a great texture and deep flavor. This one is a keeper because healthy casseroles have become an oxymoron but this one is certainly the exception. Thank you so much for this one! 😉

    1. The Clean Eating Couple says:

      So glad you liked it, Griff! Thank you so much!

  19. 5 stars
    I ordered my groceries online for this so I received 2 lbs. of chicken. I don’t cook so I felt like this was going to be hard to make for me, but this was actually super easy. The chicken took the full amount to cook since I had to stack the 2lbs of chicken, but now I have lunch for the whole week. It smells delicious and tastes so good. I did forget the salt and pepper (whoops) but I can add that when I warm up my meal. Thanks for another great meal idea, Liz!

    1. The Clean Eating Couple says:

      So glad you liked it Berni! Thank you!

  20. Hayley Navey says:

    5 stars
    So good! Easy to make, super delicious, and really filling!