Bringing the sizzling flavors of your favorite Mexican restaurant right to your dinner table, our Clean Keto Chicken Fajita Casserole is a delightful twist on classic chicken fajitas that will satisfy the whole family. This delicious casserole combines tender rotisserie chicken, colorful bell peppers, and onions, all coated in a homemade fajita seasoning that will transport your taste buds to south-of-the-border bliss.
Incorporating the principles of clean eating and low carb diets, this easy weeknight dinner is the perfect choice for those looking to indulge in the mouthwatering flavors of traditional Mexican cuisine while staying true to their nutritional goals.
Say goodbye to carb-heavy tortillas and hello to a wholesome chicken fajita bake that's as satisfying as it is guilt-free. It is so easy that it is the perfect meal to add to your weekly meal prep!
As you dig into each forkful of this hearty casserole, you'll be treated to the irresistible aroma of juicy chicken mingling with the vibrant colors of bell peppers and onions.
But that's not all—our Clean Keto Chicken Fajita Casserole takes things to the next level with layers of organic gooey cheese blanketing the entire dish, adding that perfect touch of comfort and indulgence.
Whether you're a dedicated follower of the ketogenic diet or simply someone who appreciates a delicious twist on a classic, this recipe is tailored to bring joy to your taste buds and nourishment to your body.
So, let's roll up our sleeves, gather our simple ingredients, and dive into the creation of a dish that will make you forget all about your favorite Mexican restaurant—because the best flavors are often found right in your own kitchen.
I am always looking for healthy and low-carb versions of some of our favorite recipes and this rendition did not disappoint!
This dish was inspired by our Keto Sour Cream Chicken Enchilada Casserole. Since we love fajitas as much as we love enchiladas, it was a no-brainer! Be sure to try our Keto Green Chile Chicken Casserole too! Love fajitas? Try our leftover steak fajita recipe- its soo easy. You can also enjoy spinach artichoke chicken in a keto casserole! Seriously also consider our favorite Bacon Ranch Chicken and "Rice" Casserole- it is SO GOOD!
If you like to wrap your fajitas in a tortilla, you can always look into some low carb tortillas with clean ingredients, add organic black beans as a side, or serve it on a bed of cauliflower rice. We prefer to serve our fajita chicken casserole with a simple green salad on the side with homemade dressing.
Check out our clean keto diet guide and free meal plan here!
Before setting out to prepare or consume a meal, it is helpful to set clear intentions to get the most out of the process and program our bodies for exactly what we want to receive.
Setting intentions helps to direct and focus energy to what we are trying to accomplish and our cells work to help us accomplish these goals!
If you'd like to learn more about setting intentions, check out our intentions and affirmations guide! Here are some examples of intentions:
Now let's grab that ingredient list and head to the grocery store for the best quality clean keto ingredients for our easy chicken fajita casserole that will nourish and satisfy the entire family.
Cooked Chicken: Buy a pre-cooked organic rotisserie chicken and shred it up for easy and quick use. Otherwise, get boneless skinless chicken thighs or breasts and cook them in the instant pot or slow cooker for fresh tender chicken to shred.
Avocado Oil: We use this oil because it has a high smoke point and neutral flavor to saute the onions and peppers. Check out this helpful article with info on how to pick the best avocado oil. You can also use extra virgin olive oil if you keep the temperature at medium heat or below as olive oil has a lower threshold for heat before it turns rancid.
Bell Peppers: For a colorful meal with a variety of phytonutrients we recommend getting one of each color- a red, yellow, orange, and green bell pepper! Also, be sure to opt for the organic variety to avoid unnecessary carcinogenic pesticide use. These peppers and the onions are the hallmarks of traditional fajitas that give this recipe an authentic taste and texture.
Yellow Onion: You can also use a sweet onion or a red onion depending on your taste preferences.
Diced Tomatoes w/ Green Chiles: Be sure to find an organic brand that has BPA-free cans.
Fage 5% yogurt: This full-fat yogurt comes from a great brand. It also adds a thick and creamy consistency that is similar to cream cheese but without the potential additives that come in a lot of commercial cream cheese brands.
Shredded Cheese: Either Monterey Jack or Mexican Blend works well. Be sure to get organic cheese and check the ingredients. A lot of pre-shredded cheese comes with additives and hidden starches which can potentially derail a keto diet if you aren't careful. It is always best to get a block of cheese and shred it yourself to avoid this potential pitfall.
For the Homemade Fajita Taco Seasoning: Check the ingredients on the back of every seasoning. Whenever possible, find spices that are organic from reputable companies. The only thing on the label should be a spice!
Chipotle Chili Powder
Pink Himalayan Salt
Pure Monk Fruit (optional)
Fresh Lime Juice
See the recipe card for quantities.
1. Preheat oven to 350F. Place shredded chicken in a large bowl. Heat oil in a large skillet and saute sliced peppers and onions.
2. Add sauteed onions and peppers to the chicken bowl and stir.
3. In a separate bowl mix together the can of diced tomatoes with yogurt, half of the shredded cheese (1 cup), and all of the seasonings.
4. Combine the sauce mixture with the chicken mixture and mix together well. Pour the mixture into a medium casserole dish or baking dish and evenly top it with the remaining cup of cheese. Place in the oven for 20-25 minutes or until cheese is melted and starting to brown.
Let cool for 1 minute and serve with your choice of toppings. Enjoy!
Hint: If you use a cast-iron skillet to sautee the veggies, you can transfer the mixture back into that and put it in the oven to save on clean-up!
Substitutions and Variations
For a vegetarian meal, consider using jackfruit instead of chicken. You can also add black beans and omit the chicken altogether.
If you do not have a can of diced tomatoes and chilies, consider substituting them with a cup of salsa.
Cream Cheese, a dollop of sour cream, or other full-fat yogurt brands can be used to create the creamy sauce.
If you do not have all of the seasonings, it is okay to substitute with a store-bought fajita seasoning packet. It is important to remember to check the ingredients and purchase organic whenever possible to avoid unhealthy ingredients.
If you are not on a strict low carb diet, you can add this casserole to an organic or sprouted grain tortilla. There may also be some low carb tortillas that will fit into a keto diet.
For more or less spiciness simply omit or add more cayenne or chili powder, per your personal preferences.
If you want to make ahead for a meal prep, save some leftover chicken for your next dinner!
Alternatively, you can cook chicken in the oven or on the grill or stove and cut it into bite-sized chunks as opposed to shredding it.
Leftover Keto Chicken Casserole can be stored in a glass airtight container in the fridge for up to 4 days. It can also be frozen in a freezer-safe container for 4-6 months.
It is best to avoid using plastic wrap or aluminum foil in order to avoid chemicals from leeching into the food.
Glass, Stainless Steel, or Pyrex is always the best choice when it comes to storing food.
Customize your Clean Keto Chicken Fajita Casserole by experimenting with different types of cheese. While Monterey Jack and Mexican-style cheeses are classic choices, you can elevate the flavor profile by using a combination of cheddar, pepper jack, or even a sprinkle of crumbled queso fresco. The cheese selection can add a unique twist to your casserole, making each bite a delightful surprise that brings out the best of your homemade Mexican masterpiece.
Mexican food like fajitas can easily be transformed into low-carb keto recipes by making simple swaps or omitting carbohydrate-rich ingredients like tortillas. After trying our low carb chicken fajita casserole, you won't even miss your old tortilla wraps! It is a family favorite in our home and one of many that is proof that you can eat low carb and still eat many of your favorite foods.
The vegetables in fajitas are onions and bell peppers. Most vegetables are low in carbohydrates, including peppers and onion. The vegetables that tend to be higher in carbohydrates are corn and root vegetables like potatoes, carrots, and beets.
Some spices and seasonings have a few carbs in them, especially when they are not pure or organic. However, the amount of net carbs in spices is typically negligible, especially when used in moderation.
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Looking for other casserole recipes, keto recipes, or clean eating recipes? Try these:
Learn more Clean Keto Tips and Recipes:
Clean Keto Chicken Fajita Casserole
- 3 cups shredded chicken
- 1 teaspoon avocado oil
- 4 bell peppers (one red, yellow, orange, and green) cut into thin strips
- 1 small yellow onion thin short slices
- 1 can diced tomatoes with green chilies
- 5 oz full fat yogurt Fage 5%
- 2 cup Monterey Jack or Mexican style cheese shredded and divided
- 1.5-2 teaspoon chipotle Chile powder
- ½ teaspoon pink Himalayan salt
- ½ teaspoon smoked paprika
- ¼ teaspoon black pepper
- ½ teaspoon onion powder
- ½ teaspoon garlic powder
- ½ teaspoon oregano
- ½ teaspoon ground cumin
- ⅛ teaspoon cayenne powder
- 1 pinch pure monk fruit powder (optional)
- Preheat oven to 350 F place shredded chicken in a large bowl, set aside. Heat avocado oil in large skillet over medium heat until oil glistens. Add sliced peppers and onions. Sauté for 5-7 min or until softened.
- Remove from heat and toss in with the shredded chicken and set aside.
- In a medium bowl mix together fage 5% Greek yogurt, crushed tomatoes, all of the powdered seasonings, 1 cup shredded cheese and stir to combine.
- Add the sauce mixture to the chicken mixture and stir together. Place the entire fajita mix together in a casserole dish and top with the remaining shredded cheese. Place in the oven for 25-30 min until cheese is slightly golden and melted. Let cool for 1 min. Garnish with cilantro and top with your choice of toppings. Serve warm.
Do you prefer to eat low carb dinners? This is one of our favorites! If you have any comments or questions, we would love to hear them in the comments below! Don't forget to subscribe to our newsletter for more up-to-date clean keto, clean eating, and holistic nutrition tips, recipes, and courses coming soon! Follow us on social media, we'd love to see you there!