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Homemade healthy chicken enchiladas are made with a rich red sauce tossed with tender chicken and Mexican spices. Roll the filling and bake them with a layer of melty cheese. The whole family will love this easy dinner!

Do you love enchiladas? Make shredded beef enchiladas, Instant Pot chicken enchiladas, or ground turkey enchiladas next.

healthy chicken enchiladas pulling out of a pan
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Of every cuisine out there, Mexican food will always be my favorite. I’ve spent hours testing and perfect Mexican recipes because the flavors, textures, and dishes are unmatched.

Why You’ll Love these Healthy Chicken Enchiladas

  • Hearty and filling
  • Easy to prep ahead of time
  • Kids love them!
  • Simple to customize with fillings and toppings
  • Full of protein and fiber

Ingredients and Brands I Love

Note: the full ingredients list, including measurements, is provided in the recipe card at the bottom of this post.

  • Shredded chicken: I seared mine quickly over the stove, but you could use rotisserie chicken or pre-cooked frozen shredded chicken.
  • Mexican spices: cumin, garlic powder, salt, and pepper.
  • Onion and garlic
  • Black beans
  • Green chiles
  • Enchilada sauce: you can make your own enchilada sauce for the ultimate healthy chicken enchiladas! I also love Siete’s sauce or El Pato for quick options.
  • Tortillas: regular tortillas, gluten-free tortillas, Siete grain-free tortillas, or corn tortillas all work in this recipe.
  • Cheese: Shredded Mexican cheese is my favorite. You can also use a cashew queso to keep them dairy-free.
  • Toppings: my favorites are cilantro, avocado, tomatoes, sour cream (or plain Greek yogurt), and jalapenos.
healthy chicken enchilada ingredients

Step by Step Instructions

Here are the basic steps, with images, for this edible cookie dough recipe. Skip down to the recipe card for the full printable recipe.

  1. Cook the chicken: Season the chicken on both sides then cook in a saute pan or skillet over medium high heat. Cook for 6-7 minutes on each side then remove from heat, cool and shred.
  2. Make the filling: Next, cook the diced onion and garlic until translucent then add the rest of the filling ingredients, including the shredded chicken.
  3. Fill and top the tortillas: Warm the tortillas in the microwave (other warming options: bake, fry, or char them) to make them pliable, then fill them evenly with the chicken mixture. Roll them up and place them seam side down in a asserole dish  bowl with the enchilada sauce then fill the tortilla with filling, roll and place seam side down in a 9×13 inch casserole pan. Top with enchilada sauce and cheese.
  4. Bake: bake the healthy chicken enchiladas at 350°F for 15 minutes, until heated through and the sides are bubbling.
how to make healthy chicken enchiladas

How to Cook Shredded Chicken for Enchiladas

Sear the chicken, as directed, to cook it through and shred with forks. Pound the chicken breast thin to cook it faster.

Making it in the slow cooker is an easy, hands-off approach. Add the chicken to the crock pot and cover with water or broth. Cook on low for 4-6 hours, drain, and shred.

Instant Pot shredded chicken yields ultra juicy chicken in much less time. Add the chicken breast to the Instant Pot with 1 cup of water or broth. Pressure cook for 10 minutes followed by a 5 minutes natural release. You can also cook chicken breast from frozen in the Instant Pot.

Need to save time? The easiest option is to buy it pre-cooked and shredded. I love rotisserie chicken for enchiladas because it’s fast and juicy. Most grocery stores also carry pre-cooked shredded chicken in the deli or frozen.

Recipe FAQs

What can I put in enchiladas?

Enchiladas are one of those recipes that can be a blank canvas. Use classic ingredients like chicken, beef, beans, corn, rice, sweet potatoes and more.

What makes these healthy?

At their base form, enchiladas are a healthy recipe made with protein, carbs and fats. But like many recipes, some are healthier than others, depending on the ingredients you use and their overall nutritional profile. These enchiladas use homemade gluten-free enchilada sauce or Siete enchilada sauce, black beans (fiber!), and protein-rich shredded chicken.

What tortillas to use?

I’ve tested this recipe several times, with different types of tortillas. Flour tortillas stand up well to the sauce and don’t get soggy. The same goes for a quality gluten-free tortilla. Corn tortillas are the authentic route and hold up well, especially if you fry them frist. For a grain-free option, try Siete tortillas.

healthy chicken enchiladas in a casserole dish with avocado and tomato

Serving Suggestions

Make sure you have a handful of enchilada toppings ready for everyone to pick their favorites. I love cilantro, sour cream, quick Mexican pickled onions, avocado, avocado lime crema, tomatoes, copycat chipotle corn salsa, jalapenos, and red onion.

Sides: black beans, cilantro lime rice, cauliflower rice, tomato avocao salad, roasted or mini peppers.

Drinks: skinny spicy margarita!

 If you make this recipe, I’d love for you to give it a star rating below. You can also tag me on Instagram so I can see it!

More Mexican Recipes

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4.58 from 26 votes

Healthy Chicken Enchiladas

Prep: 20 minutes
Cook: 15 minutes
Total: 35 minutes
Homemade healthy chicken enchiladas are a go-to dinner in our house. They’re made with a rich red sauce and the whole family will love this easy meal.

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Servings: 6 servings


  • 2-3 tablespoons olive oil
  • 1 lb boneless skinless chicken breast
  • 1 1/2 teaspoons cumin
  • 1 teaspoon garlic powder
  • 1 teaspoon salt
  • 1/2 teaspoon black pepper
  • 1 yellow onion diced
  • 3 cloves garlic minced
  • 1 (15 ounce) can black beans drained and rinsed
  • 1 (4.5 ounce) can diced green chilis
  • 3 cups red enchilada sauce homemade or storebought (I like Siete)
  • 12 whole wheat, grain-free, gluten-free, or corn tortillas (I like Siete grain-free tortillas)
  • 1 cup shredded cheddar cheese or dairy-free cashew queso
  • Toppings: cilantro, sour cream, diced jalapenos, diced avocado, chopped tomatoes


  • Preheat oven to 350°F and spray a large 9×13 inch casserole dish with cooking spray. Set aside.
  • Heat olive oil in a deep saute pan over medium heat. Sprinkle both sides of chicken breast with cumin, garlic powder, salt and pepper. Add to the pan with olive oil and cook chicken over medium heat for 6-7 minutes on each side, or until it reaches an internal temperature of 165°F. Remove chicken to a cutting board to cool. Note 1 for other cooking methods.
  • To the pan, add the diced onion and garlic and cook, stirring frequently, until onions are translucent and garlic is fragrant. Add the black beans and diced green chilis to the onion and garlic and stir until combined. Reduce heat to low and allow to cook slightly while shredding the chicken.
  • Use two forks to shred each chicken breast then place in the pan with the black beans mixture. Stir to combine. Remove from heat.
  • Prepare the tortillas by heating them in the microwave for 30 seconds. This softens them and makes them more pliable to work with and roll. Dip each tortilla in a shallow bowl with 1/2 cup enchilada sauce then spoon 1/4 cup chicken and black bean mixture into the tortilla. Fold tortilla over filling and roll up. Place seam down at the end of the prepared baking dish. Repeat the process until all tortillas and filling are used and pan is full of enchiladas.
  • Top prepared enchiladas with the rest of the sauce and top with shredded cheese if using. Bake in preheated oven for 15 minutes or until sauce is bubbling and cheese is melted. Top with garnishes before serving.
Last step! If you make this, please leave a review letting us know how it was!


Note 1. Options for cooking the chicken. You can slow cook chicken breasts with a cup of chicken broth or water on low for 4-6 hours, or pressure cook it for 10 minutes with a 5 minute natural release.
Enchilada sauce: My favorite gluten-free enchilada sauce is so easy to make! I love using Siete enchilada sauce and tortillas here because they’re so clean. You can find it online, through Amazon or at Whole Foods!
Freeze: before baking, cover the enchiladas before baking with plastic wrap and foil and freeze for up to 3 months. Bake from frozen until hot and bubbly. You could also freeze baked enchiladas once they’re cooled.
Dairy-free: top the enchiladas with our creamy cashew queso.



  • 9×13 Casserole Dish


Serving: 2enchiladas | Calories: 434kcal | Carbohydrates: 48.4g | Protein: 30.6g | Fat: 13.6g | Cholesterol: 76.9mg | Sodium: 1980mg | Fiber: 9.6g | Sugar: 10g | Vitamin A: 81IU | Vitamin C: 14mg

Nutrition information is automatically calculated, so should only be used as an approximation.

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Recipe Rating


  1. Eloise says:


  2. Sandra says:

    Why does it say black bean and corn mixture when there is no corn listed as an ingredient? Please update.

  3. David says:

    Ya, corn tortillas-no bueno. Substitute flour, or make a casserole. Corn tortillas broke apart just handling them.

    1. Molly Thompson says:

      Hey David! It helps to warm the corn tortillas first before handling them! That always does the trick for me. I have a post about how to soften tortillas for enchiladas that may help!

      Otherwise, flour or a grain free tortilla like Siete works well!

  4. Jo says:

    You mention adding chicken to black bean and corn mixture but i don’t see corn as an ingredient? Just a typo?

  5. Anavi says:

    The siete sauce seems to be too liquidy! Should I be doing something like cooking it prior for it to thicken by adding a slurry or do you recommend using as is.

  6. Katie says:

    Hi, there! I’ve been taught that cheese, or more broadly dairy, isn’t PCOS friendly. It certainly gives me a lot of problems. Can you tell me what your experience has been with dairy? I would love to try some of your recipes, but the cheese is just the kicker in a lot of things like these enchiladas.

    Thanks for your help!

  7. Kara says:

    Hi Molly !
    Would I be able to make the filling in the crockpot overnight then assemble them to go in the oven tomorrow?
    Thanks for the recipe !

    1. Molly Thompson says:

      Hi Kara! Yes, that’s a great idea. You could easily make the chicken in the crock pot. I want to do that now!

  8. Stephanie says:

    3 stars
    Good flavor and tasted healthy, but the corn tortillas broke apart so it ended up being more like a enchilada casserole! That was the only bummer for the presentation and ease of eating.

    1. Molly Thompson says:

      Thanks, Stephanie! Corn tortillas are definitely more fragile. It also depends on the brand of corn tortillas. If you warm the tortillas first in the microwave that can help make them more pliable when you’re rolling them. We also love Siete almond flour tortillas that hold well.

  9. Lenny says:

    I carry on listening to the news speak about getting boundless online grant applications so I have been looking around for the most excellent site to get one. Could you advise me please, where could i acquire some?