These healthy enchiladas are packed with lean protein, fiber-rich black beans, wholesome tortillas, and a bold red enchilada sauce, and finished with just enough cheese to keep them comforting without feeling heavy. They’re family-approved, freezer-friendly, and perfect for a balanced weeknight dinner.
If you’ve ever wondered how to make enchiladas healthier without sacrificing flavor, this is the recipe. They’re filling, but still taste like real-deal comfort food.
What Makes These Enchiladas Healthy?
These enchiladas are healthier because they focus on protein, fiber, and whole ingredients while skipping heavy cream-based sauces and excess cheese. Here’s how:
- Lean protein: Chicken breast keeps them high-protein and satisfying.
- Fiber boost: Black beans add fiber to support fullness.
- Smarter tortillas: Use whole wheat, gluten-free, corn, or grain-free tortillas.
- Lighter cheese approach: Just enough cheese for melt and flavor, without overload.
- No heavy cream sauce: A bold red enchilada sauce keeps them flavorful without added richness.
They’re hearty enough to satisfy but won’t leave you feeling sluggish.
It’s one of my favorite Mexican recipes I’ve shared!
Do you love enchiladas? Make shredded beef enchiladas, Instant Pot chicken enchiladas, or ground turkey enchiladas next.
Why You’ll Love These Healthy Chicken Enchiladas
- Hearty and filling without being heavy
- High in protein and fiber
- Easy to prep ahead
- Freezer-friendly
- Flexible for gluten-free or dairy-free diets
- Kid-approved
If you love enchiladas, you’ll also want to try my shredded beef enchiladas, Instant Pot chicken enchiladas, or ground turkey enchiladas next.
Reader Reviews
⭐️⭐️⭐️⭐️⭐️ “Delicious and so easy!! Used the Siete enchilada sauce and it was awesome!!” – Shelley
Ingredients You’ll Need
- Shredded chicken (rotisserie works great on a time crunch)
- Onion and garlic
- Black beans
- Green chiles
- Cumin and garlic powder
- Red enchilada sauce (homemade enchilada sauce or Siete/El Pato)
- Whole wheat, gluten-free, corn, or grain-free tortillas
- Shredded cheddar or dairy-free queso
Simple ingredients. Big flavor payoff!
How to Make Healthy Enchiladas
Step 1: Cook and Shred the Chicken: Season chicken with cumin, garlic powder, salt, and pepper. Cook 6–7 minutes per side until it reaches 165°F, then shred
Shortcut: Rotisserie chicken saves serious time.
Step 2: Make the Filling: Sauté onion and garlic until translucent. Stir in black beans and green chiles. Add shredded chicken and combine.
The filling should be moist but not watery.
Step 3: Warm the Tortillas (Don’t Skip This): Warming tortillas makes them pliable and prevents cracking. Microwave for 30 seconds before assembling.
Step 4: Assemble the Enchiladas: Dip each tortilla briefly in enchilada sauce, add about ¼ cup filling, roll tightly, and place seam-side down in a greased 9×13 dish.Pour remaining sauce evenly over the top and sprinkle with cheese.
Step 5. Bake: Bake at 350°F for 15 minutes, until the sauce is bubbling and cheese is melted. Top with cilantro, avocado, tomatoes, or Greek yogurt before serving.
How to Prevent Soggy Enchiladas
Soggy enchiladas usually happen when tortillas are oversaturated or the sauce is too thin.
Here’s how to avoid it:
- Warm tortillas first so they don’t tear. Here’s 3 ways to soften tortillas for enchiladas.
- Dip quickly, don’t soak them.
- Use a thicker red enchilada sauce (my gluten free enchilada sauce is elite).
- Bake just until heated through, not excessively long.
These small steps make such a big difference!
Make-Ahead and Freezer Instructions
Make Ahead: Assemble fully, cover, and refrigerate up to 24 hours before baking.
Freeze Before Baking: Wrap tightly in plastic wrap and foil. Freeze up to 3 months. Bake from frozen until hot and bubbly.
Freeze After Baking: Cool completely, then freeze in portions for easy lunches.
This is one of my favorite meal prep dinners because it reheats beautifully. I also love to take it to my post-partum friends!
Best Tortillas for Healthy Enchiladas
Flour tortillas hold up the best and resist sogginess, but check the ingredient list (some brands are better than others). Whole wheat would be a good option, or if low-carb is important to you, find a fiber-rich tortilla.
Corn tortillas are authentic and sturdy, especially if lightly fried first.
Grain-free tortillas (like Siete) are my go-to choice because we usually have them on hand. You especially need to warm them properly for them to work.
The key is pliability before rolling or else they’ll break and crack.
Serving Suggestions
Toppings: Cilantro, sour cream, quick Mexican pickled onions, guacamole, avocado lime crema, tomatoes, copycat chipotle corn salsa, or jalapenos
Sides: Cilantro lime rice, cauliflower rice, cucumber tomato avocado salad, or roasted mini peppers.
Drinks: Skinny spicy margarita, hot honey margarita, cucumber margarita, or a tequila mule.
FAQs
You can swap in shredded beef, ground turkey, sweet potatoes, rice, or corn. Enchiladas are flexible, just keep protein + fiber in mind for balance.
They can be! Use certified gluten-free tortillas and sauce.
Yes. Use my favorite dairy-free cashew queso (I do this all the time!) or store bought dairy-free cheese. The red sauce keeps them flavorful even without traditional cheese.
Protein will vary based on tortilla and cheese choice, but chicken and black beans provide a strong protein base per serving, yielding roughly 30g of protein per serving.
Healthy enchiladas don’t have to taste like diet food! With lean protein, fiber, bold sauce, and smart ingredient swaps, this version delivers comfort and balance in one pan.
They’re practical enough for a Tuesday night and good enough to serve guests.
Healthy Enchiladas
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Ingredients
- 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
Instructions
- 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.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
- 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 chiles to the onion and garlic and stir until combined. Reduce heat to low and allow to cook slightly while shredding the chicken.1 yellow onion, 3 cloves garlic, 1 (15 ounce) can black beans, 1 (4.5 ounce) can diced green chilis
- 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.3 cups red enchilada sauce, 12 whole wheat, grain-free, gluten-free, or corn tortillas
- 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.1 cup shredded cheddar cheese, Toppings: cilantro, sour cream, diced jalapenos, diced avocado, chopped tomatoes
Notes
Optional toppings: Fresh cilantro, sour cream or greek yogurt, diced jalapeños, green onions, diced red onion, diced avocado, chopped tomatoes, salsa or guacamole More spice. Add chili powder or jalapeños for extra flavor and spice. 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. Dipping tortillas: When dipping tortillas in the sauce, work quickly to avoid over-saturation. Corn tortillas: If using corn tortillas, lightly warm or pan-fry briefly to prevent tearing. Meal-prep: store enchiladas in individual airtight containers for easy reheating.
Video
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
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Delicious and so easy!! Used the Siete enchilada sauce and it was awesome!!
So glad you loved it. Thanks for sharing, Shelley!
Great!
Why does it say black bean and corn mixture when there is no corn listed as an ingredient? Please update.
Ya, corn tortillas-no bueno. Substitute flour, or make a casserole. Corn tortillas broke apart just handling them.
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! https://whatmollymade.com/how-to-soften-tortillas-for-enchiladas/
Otherwise, flour or a grain free tortilla like Siete works well!
You mention adding chicken to black bean and corn mixture but i don’t see corn as an ingredient? Just a typo?
Hi,
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.
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!
I may be able to provide insight, I have PCOS, had it since I was 12 I’m 36 now. I’ve done a lot of research and I also follow kym Campbell clean eating lifestyle. From what I know it’s not that dairy is bad for PCOS, as it more so that most women who have PCOS have a dairy intolerance or allergy, and that’s why it is recommend you don’t eat it. Unless you know for certain (which is normally through an allergy test) that you don’t have a dairy intolerance/allergy, it is recommend that you stay away from dairy otherwise it is fine to have. Hope this helps.
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 !
Kara
Hi Kara! Yes, that’s a great idea. You could easily make the chicken in the crock pot. I want to do that now!
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.
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.
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