Healthy Chicken Enchiladas

These healthy chicken enchiladas are packed with flavor and nutritious ingredients! The homemade enchilada sauce is the star of this recipe.

I don’t know what it is but I love Mexican food. Maybe it’s the spice or just the overall flavor profile but I love the cuisine! I have a vegetarian enchilada bake but hadn’t shared a straight forward enchilada recipe… until now. I love this recipe and hope it becomes a staple with your families!

Two chicken enchiladas on a plate.

I think a lot of people would consider Mexican food unhealthy but the truth of the matter is, within every cuisine there are healthy options! Sure, you can order or make the heaviest, creamiest dish but you could also make some simple swaps to lower the calories and up the nutrition profile. These chicken enchiladas are the perfect example. I took the traditional recipe and upgraded a few key ingredients to make it a nutritious and delicious meal.

Chicken enchilada filling in a skillet.

Ingredients for Healthy Chicken Enchiladas

  • Whole wheat flour tortillas
  • Homemade red enchilada sauce – this is the star of the recipe in my opinion!
  • Shredded Chicken – I use my slow cooker shredded chicken recipe
  • Vegetables – corn, black beans, yellow onion, garlic and cilantro
  • Cheese – I use low-fat, shredded Mexican cheese
  • Spices – chili powder, cumin, salt
  • Toppings – scallions, cilantro and jalapeños
Two cheesy chicken enchiladas on a plate.

Prepping and Storing Enchiladas

There are a couple of different ways you can prep these enchiladas ahead of time. One big time saver is making the homemade enchilada sauce ahead of time! You can freeze it if you make it more than one week in advance, otherwise just store it in an airtight container in the fridge until you’re ready to use. You can also prep the entire meal ahead of time and then bake it when you’re ready.

Baking casserole dish with cheesy chicken enchiladas topped with jalapeño.

To store, use an airtight container and keep in the fridge for up to five days. I don’t think I would freeze the leftovers because the cheese gets a little wonky, but if that doesn’t bother you, you can absolutely try it!

How to Serve Enchiladas

When serving these enchiladas I usually have a few topping options on hand including fresh cilantro, green onions, jalapeños, sour cream or Greek yogurt, salsa, hot sauce and guacamole or fresh avocado. You don’t need all of these. Pick your favorite toppings and use those!

These chicken enchiladas are a meal on their own, but it’s always fun to have a few sides… especially if you’re hosting. Here are some options:

Two chicken enchiladas on a plate topped with cheese and cilantro.

More Healthy Mexican Recipes

Healthy Chicken Enchiladas

4 from 93 votes
These healthy chicken enchiladas are packed with flavor and nutritious ingredients! The homemade enchilada sauce is the star of this recipe.
Two chicken enchiladas on a plate topped with cheese and cilantro with a fork on the plate.
Prep Time 10 minutes
Cook Time 50 minutes
Total Time 1 hour
Servings 8


Enchilada Sauce

  • 1 teaspoon olive oil
  • 4 garlic cloves, minced
  • 2 chipotle peppers, diced (from canned chipotle peppers in adobo sauce)
  • 1 Tablespoon of adobo sauce from can
  • 1 16 oz can tomato sauce
  • 1 teaspoon dried oregano
  • 1/2 teaspoon chili powder
  • 1/2 teaspoon ground cumin
  • 1 cup low sodium vegetable or chicken broth
  • 1/4 teaspoon sea salt
  • 1/4 teaspoon fresh pepper

Chicken & Veggies

  • 1 1/2 teaspoons olive oil
  • 2 cups cooked shredded chicken, about 2 breasts
  • 1/2 cup frozen corn, thawed
  • 1/2 cup cooked black beans
  • 1/2 medium yellow onion, diced
  • 3 cloves garlic, minced
  • 1/4 cup cilantro
  • 1/2 teaspoon chili powder
  • 1/4 teaspoon cumin
  • 1/2 cup enchilada sauce, from above


  • 8 7-inch whole wheat flour tortillas
  • 1 1/2 cups shredded Mexican cheese, divided
  • green onions and fresh cilantro, for topping
  • jalapeños, for topping (optional)
  • plain Greek yogurt or sour cream, optional
  • sliced avocado, optional


  • In a medium saucepan over medium heat, add oil and sauté garlic until fragrant, about 1-2 minutes. Add chipotle peppers, adobo sauce, tomato sauce, oregano, chili powder, cumin, broth, salt and pepper. Bring to a boil. Reduce the heat to low and simmer for 5-10 minutes. This will help thicken the sauce. Set aside until ready to use.
  • Preheat oven to 400°F degrees.
  • Heat the olive oil in a medium skillet over medium-high heat. Sauté onions and garlic until soft and translucent, about 4-5 minutes. Add chicken, corn, black beans, cilantro, chili powder, cumin and 1/2 cup enchilada sauce to the skillet. Stir to combine and cook for another 4-5 minutes. Remove from heat.
  • Spray a 13 by 9-inch glass baking dish with non-stick spray. Fill each tortillas with 1/4- 1/3 cup of the chicken and black bean mixture, a sprinkle of cheese and roll it up.
  • Place rolled tortilla into the baking dish, seam side down. Once all the tortillas are filled, cover with remaining sauce and sprinkle remaining shredded cheese over top.
  • Cover with aluminum foil and bake in the oven on the middle rack for 20-25 minutes or until cheese is melted and enchiladas are warm throughout. Serve enchiladas with your toppings of choice: green onions, fresh cilantro, jalapeños, sliced avocado and Greek yogurt and/or sour cream.



Serving: 1enchilada without toppings Calories: 288kcal Carbohydrates: 34g Protein: 18g Fat: 9g Sodium: 753mg Fiber: 6g Sugar: 3g
Course: Lunch/Dinner
Cuisine: Mexican
Keyword: healthy chicken enchiladas


Please leave a comment and star rating on this post and share on social media using the hashtag #eatingbirdfood. I love seeing your recipe shares!
This post may include affiliate links. Thank you for your support.

Leave a Comment

Your email address will not be published. Required fields are marked *

Recipe Rating

    1. Vandana
      August 18, 2021 AT 5:06 am

      5 stars
      Very nice recipe. We don’t get chipotle peppers hence I added the sauce with Mexican flavoured tomatoes to make the sauce. Very nice and loved by family. It’s a keeper. Thank you for sharing.

      1. Brittany Mullins
        August 18, 2021 AT 10:51 am

        Yay! This makes me so happy to hear, Vandana! So happy these enchiladas were a hit. Thanks for the review and star rating. It means so much to me!

    2. Heather
      August 16, 2021 AT 5:12 pm

      Can these be made and frozen in advance to cook at a later time?

      1. Brittany Mullins
        August 18, 2021 AT 8:16 pm

        I haven’t tried freezing these, but I would imagine they’d freeze just fine to cook at a later time! Let me know if you end up trying it and how they turn out.

    3. Marcin Staniszewski
      August 5, 2021 AT 11:45 am

      4 stars
      good recipe but your ingredient list is confusing.

      1. Brittany Mullins
        August 5, 2021 AT 11:50 am

        Can you explain why it’s confusing? Would love to be able to fix it!

    4. Jamie Alexander
      August 4, 2021 AT 5:34 pm

      5 stars
      Such an amazing, easy recipe.

      I found I only needed one chipotle pepper. Also, bought rotisserie chicken from the store and shredded it vs making it & was a huge time saver.

      1. Brittany Mullins
        August 5, 2021 AT 11:05 am

        I’m so glad these enchiladas were a hit, Jamie! Thanks for the review. I really appreciate it!

    5. CounselorChick
      June 21, 2021 AT 2:52 pm

      4 stars
      2 chipotle peppers must be too spicy for most people. I used 1 1/2 and it was verging on too much spicy for my guests. Otherwise, great recipe!

Parchment paper lined with protein balls.


Eating healthy doesn’t have to be boring!



Subscribe to our list and get your free printable PDF of the 3 Day Clean Eating Meal Plan and Shopping List!