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!

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

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 You’ll Love This Recipe

• 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, making low carb chicken enchiladas, 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!

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.
• For the filling: Shredded chicken – here is how to cook chicken breast in Instant Pot. Low sodium black beans (cooked dried beans or Instant Pot 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 baked chicken breast 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.

How to Make Healthy Chicken Enchiladas

• 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 Instant Pot 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 healthy 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

What to Serve With Healthy 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:

• Mexican kale salad
• Homemade guacamole
• Instant Pot refried beans

How to Store

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.

More Favorite Mexican Recipes

• Skillet beef enchiladas
• Chicken enchilada skillet
• Slow cooker chicken enchilada casserole
• Mexican chicken and rice
• Chicken tostadas
• Chicken burrito skillet
• Taco skillet
• Baked tacos
• Creamy chicken enchilada soup