I’m sharing our absolute family favorite Mexican inspired dinner idea. These nutritious and delicious Healthy Chicken Enchiladas are stuffed with shredded chicken, beans, and green chiles, baked with the best homemade enchilada sauce and bubbly cheese!

This is a melt-in-your-mouth, restaurant-quality, easy family-friendly dinner! Just like our favorite chicken quesadillas and chicken burritos.

Healthy chicken enchiladas on a plate with sour cream and cilantro.

If you’ve ever ordered a mouthwatering cheesy chicken enchilada at a Mexican restaurant and wondered if you could ever make something like that at home (but maybe a healthier version), the answer is a big ‘ol yes!

This easy Mexican-inspired recipe is one of most popular, delicious and filling healthy dinners in our house.

It’s made with tortilla rolls stuffed with seasoned juicy chicken, beans, green chiles, cheese, and a homemade enchilada sauce topped with even more cheese and sauce and baked until bubbly! Healthy comfort food at its finest is the epitome of what our family likes to eat!

You may also love to browse these 65 healthy chicken recipes!

Why Is Shredded Chicken Enchiladas Recipe Healthy?

  • Loads of fresh ingredients: Onions, garlic, black beans, and toppings like avocados, and freshly grated cheese are all a part of what makes this dish so tasty and so healthy.
  • Customize it: There are ways to make chicken enchilada recipe even healthier by choosing low sodium canned ingredients, using a bit less of the cheese, using whole wheat tortillas, and avoiding any toppings that don’t work for you. 
  • Plain yogurt: Although we do enjoy a bit of sour cream as a topping, in the enchilada filling itself, we use yogurt!
  • Baked not fried: Some recipes require you to fry your tortilla shell a bit to prevent soggy shells. This one avoids all of that excess grease!

Need a lower in carbs Mexican enchiladas recipe? Check out chicken zucchini casserole or low-carb chicken enchiladas!

Ingredients for Healthy Chicken Enchiladas

  • Shell: Whole wheat, white or gluten-free tortillas of medium size will work. I found these 50% corn/50% wheat tortillas and they have a flavour of corn and the flexibility of flour dough.

Casa Mendosa tortillas in packaging.

  • For the filling: Shredded chicken (cooked boneless chicken breasts). Low sodium black beans, diced green chiles, plain yogurt, shredded cheddar, or Tex Mex cheese. Homemade enchilada sauce.

Use leftover chicken! This is a great time to use up any leftover cooked chicken you’ve prepared for previous dinners. Nothing goes to waste in my kitchen!

  • Enchilada sauce: Chopped onion, minced garlic, chipotle in adobo pepper, minced. Flour. Oil for frying. Tomato sauce with, low sodium or preferably no salt added.
  • Optional toppings for serving: Green onion, avocado, and sour cream.
  • Cooking spray: I use Misto, but you can use whatever you have on hand.
Tortillas, tomato sauce, chicken breast, yogurt, avocado, black beans, green onion, cilantro, cheese.

How to Make Chicken Enchilada Recipe

  • Prep: Cook chicken breasts (I usually make Instant Pot chicken breast) or use leftover rotisserie chicken, and shred it.
  • Make homemade enchilada sauce: Sauté onion and garlic in oil, then add chipotle pepper in adobo with flour, and whisk to combine. It’s gonna be lumpy. Then add the tomato sauce, whisk and simmer for a few minutes. It’s ready!
  • Prep: Time to crank up the oven to 350 degrees F and spray 9 x 13 baking dish with cooking spray.
  • Make the filling: In a large bowl, combine shredded chicken, black beans, green chiles, some cheese, yogurt, and 2 cups of enchilada sauce. Stir, taste, and now is the time to adjust salt if you used no salt added tomato sauce. Otherwise, it should be fine.
  • Fill tortillas and roll: Scoop about 1/2 cup chicken mixture and spread onto a flat tortilla. Roll it up and place seam side down in sprayed baking dish. Do this with the remaining tortillas until you have about 11-12 rolls. They should be rolled tight enough to allow this many to fit.
  • Season the top of casserole: Top the rolled enchiladas with remaining chicken enchilada recipe sauce and sprinkle with remaining cheese. Make sure to spread evenly and each roll gets its fair share.
  • Bake: Spray inside of a piece of foil you will be covering the dish with, or I prefer a silicone lid, with cooking spray, so it doesn’t stick to the precious cheese, and cover. Bake your Mexican chicken enchilada recipe for 20 minutes, then uncover (carefully) and bake until cheese is melted and bubbly.
  • Let enchiladas sit before serving: Remove from the oven, cover again and let rolls absorb all the delicious sauce and allow the flavours settle for about 10 minutes. Again, remove the cover carefully not to “rip off” the cheese.

Garnish it! If you’re a cilantro lover sprinkle some fresh cilantro on top just before serving. Some people like the citrus note of a squirt of lime juice too!

Optional Add-In’s and Variations

  • Rotisserie chicken: Precooked rotisserie chicken will also contain more sodium than breast cooked at home, but if this is of no concern to you, then, by all means, use it!
  • Beef instead of chicken: For a beef enchilada alternative, use some leftover taco meat or fajita filling.
  • Beans: Black beans are a classic filling, however, feel free to substitute for pinto beans, lentils, or even refried beans.
  • Vegetarian: For a meatless option, swap out the chicken for loaded veggies, such as mushrooms, zucchini, or peppers. Load it up with extra beans and cheese, like veggie quesadillas!
  • Vegan: Try these vegan enchiladas from my friend Anjali of Picky Eater Blog – they look amazing!
  • Spices: Switch up the spices to suit your tastes. Some possibilities for added seasoning are cumin, chili powder, garlic powder (if you don’t have fresh on hand), and even some herbs like oregano.
  • Cheese: If you can get your hands on some Mexican cheese like queso fresco, it’s great to have some crumbled on top.

Looking for more Mexican Inspired dishes to complete your menu? Try carne asada steak or chicken tortilla soup.

Tips for Best Results

  • Corn tortillas: Use flour tortillas if you can help it. Many store-bought corn tortillas break easily. Unless you know the trick. I have heard of warming them up in a microwave but had no success with this method. However, homemade corn tortillas will roll with no problem.
  • To keep sodium in check: Many store-bought ingredients contain a bit of sodium in this chicken enchiladas recipe. Do your best to keep added salt to a minimum wherever you can. Using a “no salt added” tomato sauce allows you to maintain a lower sodium content.
  • Amount of filling. Don’t overstuff your shells. They will be hard to roll (no matter how soft they are), there’s a chance of having too much sauce in there making them too soggy, and it’ll be quite the mess.

FAQs

Why are my enchiladas soggy?

When using soft flour tortillas for Mexican chicken enchiladas recipe there is always a chance of this happening. However, if it’s extra soggy it could be due to a couple of things. The first is that you may have added too much filling, especially if your filling is very saucy. Cheese also produces oil, which may seep into your tortilla if you have used more than instructed. Overdoing the topping of cheese and sauce is also one of the main reasons it can get soggy.

Why did my enchiladas fall apart?

Soggy shells will definitely cause your enchiladas to fall apart. Either that or too much filling, and if you didn’t bake with the seam side facing down, well you’re probably in for a messy ride!

How to keep tortillas from breaking when making enchiladas?


Keeping them soft is key. Corn tortillas are sturdier and will need a little more attention in this area. If you keep your tortilla shells (flour or corn) in the fridge, bring them to room temperature before using them. If they are too cold, they will not be as pliable.

Can I bake enchiladas without foil?

You can, but keep in mind the top could overbake before the inside catches up. The edges of the tortilla shells may dry out a bit too.

Healthy chicken enchiladas in baking dish topped with fresh cilantro.

What to Serve With Shredded Chicken Enchiladas?

To serve, place Mexican chicken enchiladas recipe on a plate and top with your favorite toppings like sour cream or yogurt, cilantro, and avocado.

Also these sides would go well:

How to Store Mexican Chicken Enchilada Recipe?

Store leftovers: Keep enchiladas covered in an airtight container in the fridge for up to 3 days. Or if you have room, just cover the baking dish and refrigerate like that. Another reason to love silicone covers!

Reheat: Reheating leftovers in a microwave is the best way. Or, if you would like to reheat in a baking dish, add a splash of water, cover, and bake at 350 degrees F until heated through.

Make ahead and freeze uncooked: It is nice to make enchiladas as a freezer meal or an extra batch. Assemble enchiladas up to the point of adding cheese on top, make sure to cool, wrap tightly with a few layers of plastic and then foil on top, and freeze for up to 3 months. To bake, thaw in the fridge overnight, and bake the next day.

Other freezer meals: If you’re looking for more ideas for family-friendly freezer meals, check out buffalo chicken chili, ground turkey taco soup, chicken burritos, and ground chicken tacos. Meal prep is not only convenient but it also helps make healthy food choices easier!

More Favorite Mexican Recipes

Two healthy chicken enchiladas on a plate with sauce, cheese and sour cream.
healthy chicken enchiladas recipe

Healthy Chicken Enchiladas

I'm sharing our absolute family favorite Mexican inspired dinner idea. These nutritious and delicious Healthy Chicken Enchiladas are stuffed with shredded chicken, beans, and green chiles, baked with the best homemade enchilada sauce and bubbly cheese!
5 from 3 votes
Servings 6 servings
Calories 619
Prep Time 30 minutes
Cook Time 30 minutes
Total Time 1 hour

Ingredients  

  • 1 small onion finely chopped
  • 3 large garlic cloves minced
  • 1 chipotle pepper in adobo sauce + 1 tbsp sauce minced
  • 2 tbsp any flour
  • 2 tbsp oil for frying
  • 24 oz tomato sauce no salt added
  • 3 large cooked boneless chicken breasts shredded
  • 14 oz can low sodium black beans rinsed & drained
  • 4 oz can diced green chiles
  • 1/2 cup plain yogurt
  • 1 1/2 cups cheddar or Tex Mex cheese shredded, divided
  • 12 medium whole wheat or any flour tortillas
  • Cooking spray I use Misto
  • Cilantro, green onion, avocado and sour cream for serving

Instructions 

  • Cook chicken breasts using your favorite method or use leftover rotisserie chicken. I usually make Instant Pot chicken breast.
  • In the meanwhile, make enchilada sauce. Preheat medium pot on medium heat and add oil. Then add onion and garlic, saute for 4 minutes, stirring occasionally.
  • Add chipotle in adobo pepper with sauce and flour, whisk until combined.
  • Add tomato sauce, whisk and simmer for a few minutes. Turn off heat.
  • Preheat oven to 350 degrees F and spray large 9" x 13" baking dish with cooking spray. Set aside.
  • In a large bowl, add chicken, black beans, green chiles, yogurt, 1/2 cup cheese and 2 cups enchilada sauce. Stir with spatula to combine and adjust salt to taste, if necessary.
  • Scoop about 1/2 cup mixture onto flat tortilla and wrap. Place seam side down in previously prepared baking dish. Repeat with remaining tortillas and chicken mixture and packing enchiladas tightly in a baking dish. I usually end up with 11-12 rolls.
  • Spread remaining enchilada sauce on top and sprinkle with remaining 1 cup cheese.
  • Spray inside of a piece of foil you will be covering dish with, or I prefer a silicone lid, with cooking spray, so it doesn't stick to precious cheese, and cover. Bake covered for 20 minutes. Then uncover and bake for 5-10 more minutes or until cheese has melted and is bubbly.
  • Remove from the oven, cover and let enchiladas stand for 5-10 more minutes. Serve hot with cilantro, green onion, avocado and sour cream, if desired.

Notes

  • Store: Keep enchiladas covered in an airtight container in the fridge for up to 3 days. Reheat in microwave.
  • Freezer Meal: Assemble enchiladas up to the point of adding cheese on top, make sure to cool, wrap tightly with a few layers of plastic and then foil on top, and freeze unbaked for up to 3 months. To bake, thaw in the fridge overnight and bake next day.
  • Corn tortillas: Use flour tortillas if you can help it. Many store-bought corn tortillas break easily. Homemade corn tortillas will roll no problem.
  • To keep sodium in check: Do your best to keep added salt to a minimum wherever you can. Using a” no salt added” tomato sauce allows you to maintain a lower sodium content.
  • Rotisserie chicken: Precooked rotisserie chicken will also contain more sodium than breast cooked at home, but if this is of no concern to you, then, by all means, use it!
  • Beef instead of chicken: For a beef enchilada alternative, use some leftover taco meat or steak fajita filling.
  • Beans: Feel free to substitute for pinto beans, lentils, or even refried beans.
  • Vegetarian: For a meatless option, swap out the chicken for loaded veggies, such as mushrooms, zucchini, or peppers. Load it up with extra beans and cheese!
See recipe post for more tips and FAQs.

Nutrition

Serving: 2enchiladas | Calories: 619kcal | Carbohydrates: 61g | Protein: 31g | Fat: 22g | Saturated Fat: 9g | Cholesterol: 68mg | Sodium: 507mg | Fiber: 11g | Sugar: 9g
Course: Dinner
Cuisine: Mexican
Author: Olena Osipov
Did you make this recipe?Mention @ifoodreal or tag #ifoodreal!

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About Olena

Welcome! I grew up in Ukraine watching my grandma cook with simple ingredients. I have spent the last 11 years making it my mission to help you cook quick and easy meals for your family!

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Comments

  1. 5 stars
    Looks SO great. Dying to try it! Please tell me how to adjust to serve 3 instead of 6. I hesitate to simply half everything.
    Thank you!
    Carole
    Houston

    1. You could just half everything 🙂 Or better yet – freeze half for a freezer meal, see recipe notes for directions on how to do that and then you have a meal for later too 🙂

  2. This recipe looks great and I’d like to try it, except I really don’t care for anything with chiles in adobo sauce (I think it’s thee smokiness that I don’t like). Anything I could substitute or could I just leave it out?

    Thanks

  3. 5 stars
    I’m happy to report that these enchiladas were absolutely amazing!!!

    Perfectly paired with your delicious Instant Pot refried beans. Both so easy to make, this is a big win!

    Eating leftovers tonight, yay!

  4. Hi Olena,

    I’m dying to make this recipe but I can’t find chipotle pepper in adobo sauce here in the Greater Vancouver area. Any suggestions?
    TIA

    1. Smoked paprika would be great. You can find it in Ethnic/Mexican section of Superstore and I’m sure Save on and Thrifty’s.

      1. Thank you, I looked at my local Super Store and Walmart in the Mexican section for months and couldn’t find it.
        Went to Safeway yesterday and fund it! Bought few cans 🙂

        1. Really, interesting…Maybe shortage like everything else…Yes, buying a few cans at a time is a good idea and I freeze leftovers and use as needed.

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