Healthy Enchiladas Recipe

This recipe for healthy enchiladas has a truly authentic flavor!

Enchiladas are a fabulous dish. And while they are a little time-consuming to make (about an hour for assembly on this recipe), they are not complicated at all! Think of them as baking burritos in a casserole dish with sauce. It really is that easy!

Clean Eating Enchiladas on a white plate. A single enchilada is shown up close. You can see the chicken inside with the sauce ladled over the top.

So how do you make them?

Keep in mind, the options for Enchiladas are endless. You can make them vegetarian (just beans and cheese), dairy free (as I have done here), gluten-free (simply substitute the flour in the sauce, and be sure all other ingredients are gluten-free), or with everything but the kitchen sink. The sky’s the limit. Just have fun!

You could even do an Enchilada Surprise. Simply fill different enchiladas in the same dish with different fillings. Then, the enchilada you end up with will be a surprise! Plus, you get to try lots of different variations in one dish.

More Healthy Mexican-Style Recipes

Healthy Enchiladas Recipe

Sauce recipe was adapted from a recipe on AllRecipes that is no longer on their website.

Clean Eating Chicken Enchiladas Recipe

Healthy Chicken Enchiladas

Chicken enchiladas are a Latin classic enjoyed the world over. This delicious recipe gives them a healthy upgrade without sacrificing authentic flavors.
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Course: Main Course
Cuisine: Mexican
Prep Time: 40 minutes
Cook Time: 1 hour
Total Time: 1 hour 40 minutes
Servings: 36 enchiladas
Calories: 72kcal



  • ¼ cup olive oil
  • ¼ cup. whole wheat pastry flour
  • ½ cup chili powder
  • 30 oz. canned tomato sauce (no sugar added)
  • 4 cups water
  • ½ tsp. ground cumin
  • ½ tsp. garlic powder
  • ½ tsp. onion powder


  • 36 count package corn tortillas (check ingredients!)
  • lb. boneless, skinless chicken breasts (pre-baked)
  • 45 oz. canned refried beans (check ingredients! See link above)
  • 1 batch enchilada sauce



  • Put oil, flour and chili powder in a medium to large stock pot and warm. You should have a nice paste-like substance when everything is mixed. Cook, stirring constantly for about 1 minute.
  • Add tomato sauce and water to the pot and stir.
  • Add in the cumin, garlic powder and onion powder and stir constantly for about 5 minutes. The sauce should thicken slightly.
  • Set aside.
  • NOTE: The sauce will thicken just slightly when baking. If you want a runnier sauce, add more water before pouring over the enchiladas.


  • Pre-heat oven to 350 degrees F.
  • Line two cookie sheets with parchment paper.
  • Pre-bake the chicken (I did not use any spices at all) until it reaches at least 165 F. on a meat thermometer.
  • Shred the chicken using two forks.
  • Mist a large casserole dish with olive oil (I used 3 casserole dishes. Depends on the size you use.)
  • Empty the beans out into a bowl for easy access.
  • Warm your tortillas in the microwave by wrapping them in a damp paper towel and microwave for approximately 2-3 minutes, or until soft and pliable. If you do not have a microwave, you will have to warm the tortillas on your stove top, one at a time as you work.
  • Spoon and spread about 1 tbsp (give or take) of beans on to a warmed tortilla.
  • Place the same amount of shredded chicken in the center of the tortilla and roll up (like a burrito without the ends tucked in).
  • Place, end-of-wrap side down, in a your casserole dish and repeat until the dish is full.
  • Divide the sauce between your dishes evenly.
  • Place in oven and bake for about 15-20 minutes. It’s done baking when the sauce bubbles.
  • Add any toppings you’d like. For example, Shredded cheese, low fat sour cream, shredded lettuce, guacamole, tomatoes, onions.
  • Allow to cool (the sauce will be VERY hot!), and serve.


Please note that the nutrition data is a ballpark figure. Exact data is not possible. Data does not include the enchilada sauce. Please see that recipe for that nutrition data.


Serving: 1enchilada with sauce | Calories: 72kcal | Carbohydrates: 1g | Protein: 9g | Fat: 2g | Cholesterol: 28mg | Sodium: 54mg | Potassium: 172mg | Vitamin A: 15IU | Vitamin C: 0.5mg | Calcium: 5mg | Iron: 0.3mg

This recipe from the Gracious Pantry archives, originally posted 1/22/11.

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  1. trude wofford says:

    tiffany I made some wonderful ones last week I got some( clean) green salsa in a jar and added a little chicken broth and warmed it up ( and then made a slury of cornstarch and water to thicken) this was my sauce, for my chicken I used some breasts covered them with water added some sliced onion ,garlic, carrot ,and celery and simmered till chicken was done and veg tender- after it cooled removed chicken and veg from the broth (this is the broth i used in the sauce) then chopped it all together and added some white beans and spinach rolled this into corn tortillas (cause my daughter has cd) put into a casserole dish poured the sauce over covered with tin foil and baked @ 350 about 30 min— wonderful

    1. The Gracious Pantry says:

      Trude – Sounds great! Yum!

  2. Lindsay & Steve says:

    Just wanted to drop you a quick note letting you know how absolutely DELICIOUS these were (I’m sure you know already :P) — the perfect fix at the end of a wonderful weekend! Thank you again and again for everything you do!!

    1. The Gracious Pantry says:

      L&S – You’re very welcome! I’m so happy you enjoyed them! (I need to make them again myself pretty soon. It’s nice how long they last…) ๐Ÿ˜‰

  3. Rebecca_vance says:

    I have a chicken fiesta soup recipe…all the ingredients are clean except it calls for a 10 oz. can of enchilada sauce…i haven’t found any clean canned…so i was going to make this and use it…BUT…since I only need 10 ounces of sauce…how long will this sauce keep. In the fall and winter last year (when I first found the chicken fiesta soup recipe) we ate this soup probably once a week. (however it’s just me and my husband and son that will eat it…my son is only 3 yrs old…so one crockpot of soup last for a meal and at least two meals of leftovers.) SOOOO…does it keep well in the fridge?? I’m thinking that I should probably half the recipe anyways too. I’m SO excited to try this…I can’t wait for the soup with it!! I’m SO weird with soup…we eat it SOOO much in the fall and winter…but during the spring and summer I almost can’t bring myself to make it…it just feels wrong!! Sometimes in the winter we’ll have a different soup every night of the week…my crockpot gets good use then!! ๐Ÿ™‚ (okay, sorry, you didn’t want to know my life’s story!!) ๐Ÿ™‚ THANKS!!

    1. Anonymous says:

      Rebecca – LOL!!! Love it! What I would do is make the sauce and then freeze whatever you have left over in ice cube trays. That way, you can use as much as you need when you need it. Enjoy the soup!

  4. Anonymous says:

    Dylydoodles – That’s FABULOUS!!! Congrats!

  5. Anonymous says:

    Trude – Fantastic! Let me know how it turns out!

  6. could you freeze enchilada sauce to have on hand like canned?

    1. graciouspantry says:

      Jbkidsco – I don’t see why not. Should work fine.

  7. Could you use the Clean Quinoa Tortilla’s in this recipe?

  8. Kimberly Holmes says:

    I just pinned your recipe. I am making some stuffed peppers with quinoa and black that called for enchilada sauce in a can. I knew you would have a recipe for enchilada sauce. I will let you know how they turn out

    1. The Gracious Pantry says:

      Please do!

  9. Do clean whole wheat tortillas exist?? I can’t find them anywhere! Thanks!

    1. The Gracious Pantry says:

      MrsMCoop – Yup! They sure do. What stores do you have available to you in your area?

  10. Hi! This says it makes 36…is that with the 8 inch size tortillas or with smaller ones? Does this make several dishes? Just trying to clarify! Thanks!

    1. The Gracious Pantry says:

      Laura – I’ve never seen corn tortillas that are 8 inches. These are the smaller ones. The number of dishes will depend on the size of your dishes.

  11. You have this recipe listed in your Freezer Meals category. Do you prepare, cook, cool then freeze this dish? or do you assemble it with sauce and all then freeze it? Which method would you choose?

    1. The Gracious Pantry says:

      Jennifer – You could really go either way with this one. But keep in mind how you will be reheating it. If you plan on microwaving, that can really dry out the chicken. So in that case, freezing before cooking would be good.

  12. I made these last night finally and yet another recipe on here we LOVE! I halfed the sauce and did 18 enchiladas. I did sub coconut flour (to be GF) instead of the whole wheat pastry flour..was worried that wouldn’t work but it turned out perfectly! I also added the cheese and tomatoes before cooking and it turned out amazing!

    1. The Gracious Pantry says:

      Chelsea – That’s fantastic!! So glad you enjoyed it! ๐Ÿ˜€

  13. nikkisaintlouis says:

    Could you also use the Food for life Sprouted corn tortillas for this recipe?

    1. The Gracious Pantry says:

      Nikkisaintlouis – I’m sure you could. I just don’t know if they are clean. You would have to post the ingredients here. I’ve never seen them.

  14. Shannon L says:

    I am looking for your clean chicken enchiladas recipe. I pinned a long time ago and now the pin takes me to an oatmeal recipe! HELP!!!!

    1. The Gracious Pantry says:

      Shannon L – This is the enchilada recipe…