These high protein healthy chicken enchiladas taste like the real deal with a fraction of the carbs and a ton of nutritious veggies.

Enchiladas are my comfort food. If I’m feeling down or just want a warming meal, I make enchiladas. I’ve been making various spin-off’s of this recipe for nearly a decade because there are so many tasty combinations you can cook up!
My Chicken Enchilada recipe uses a combination of chicken, veggies, enchilada sauce, and corn tortillas for a flavor-packed, nourishing, high protein, and lower carb version of the classic. With my “enchilada pie” method, it also drastically cuts down on prep time, making it a totally do-able weeknight meal.

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Recipe Highlights
- High protein. A whopping 44 grams per serving!
- Low carb. Only 22 net carbs per serving. That’s a lot lower than traditional enchiladas!
- Individual portions. Less mess when serving it up at dinner-time.
- Perfect for weeknight dinners. No pre-heating or rolling tortillas here!
- Way more veggies. My version sneaks in vegetables without sacrificing flavor.

Key Ingredients
Pre-cooked Chicken
You can use leftover chicken from a previous meal or buy some rotisserie chicken. This step helps to drastically reduce prep time while still ramping up the protein count. I like to plan on making chicken for dinner the night (or few nights) before. That way I can prep a few extra chicken breasts at the same time and pop them in the fridge to use later in the week for this recipe.
Enchilada Sauce
In my cookbook, How To Eat, I use my own homemade enchilada sauce with dried ancho chilis, onion, garlic, and tomato paste. It’s super simple and insanely packed with the classic enchilada flavors you love. Typically, I prep a few batches at a time and freeze the extra for later use. But you can use any red enchilada sauce you already have on hand or that’s available at your local grocery store.
A few good options are Hatch Red Enchilada Sauce and Siete Red Enchilada Sauce.
Corn Tortillas
This is another that I typically make at home because it’s healthier and a lot more tasty. It’s also kind of therapeutic to make your own tortillas. I love that I can make exactly the amount I need rather than buying a pack of 20 or 50 and only using 5. Homemade tortillas use masa harina which is a type of corn flour that has less anti-nutrients and is therefore better for your body than regular corn flour. The brand of masa harina I use is called Masienda.
If you don’t have the time or don’t want to make your own corn tortillas, then I recommend looking for store-bought options with minimal ingredients. Ideally, it should only have masa harina and maybe salt. Masienda has pre-made corn tortillas as well that you can find at Whole Foods, but any simple corn tortilla will work for this, too.
Because we’re only using two corn tortillas per serving, we’re able to keep the enchiladas fairly low carb. If you’re carb sensitive, then you can reduce it to one corn tortilla per serving instead.
Related: Find Out If You’re Carb Sensitive With My Free Quiz!
Veggies
I like to bulk up my enchiladas with flavorful veggies. In this version, I use bell pepper, zucchini, garlic, and onions. This combo ramps up the flavor while also sneaking in low glycemic vegetables. If you’re active then you can also add in 1/2-1 cup of black beans per serving, too. This will dramatically raise the fiber which feeds the good gut bacteria and raises satiety hormones even more!
Equipment Needed
- skillet
- four 5×7 ceramic or glass baking dishes (you can also use a 9×9 baking dish if you plan on cooking it all in one dish)
How To Make This Recipe

Sauté the zucchini, bell pepper, and onions with some olive oil and salt until softened.

Add the chicken, spices, jalapeño, and enchilada sauce and sauté for five more minutes. Sprinkle with cheese and stir in until melted.

Pour 1/4 cup enchilada sauce into the bottom of each dish.

Add the chicken and veggies mixture.

Top with tortillas, more enchilada sauce, and cheese.

Bake for 15 minutes at 400 F. Let it cool for 5-10 minutes before serving.
Ingredient Swaps
- Chicken: Other poultry works, just make sure it’s pre-cooked and shredded.
- Zucchini: Eggplant, diced carrots, or yellow squash can all be used.
- Bell pepper: Poblano pepper is mild and can be used instead of bell pepper.
- Cheese: If you’re dairy-free, just sub out the cheese. It’s not required for this recipe to taste delicious.
- If you’re very active: Add 2-4 cups black beans to the base. You can also test out adding 1-2 cups frozen corn to the base as well. Just stir either (or both) of these in when you add the chicken.
- If you’re carb sensitive: Reduce the tortillas to one per serving instead of 2.
Storing and Reheating
These leftovers store really well. Just cover any leftovers with tin foil and keep in the fridge for up to 5 days. When ready to eat, remove it from the fridge and let it sit at room temperature for 5-10 minutes while the oven preheats to 400. Keep it covered with tin foil while you heat it for 10 minutes or until warmed through.
Toppings
This recipe doesn’t require toppings, but you certainly can add them on! Below are my favorite things to add on top of these Chicken Enchiladas.
- toasted pumpkin seeds (pepitas)
- guacamole
- greek yogurt (or sour cream)
- cilantro
- diced yellow onions
- diced jalapeño
What to Pair This With
This is a full meal, so you don’t need to pair it with anything. But if you want some sides, here’s what I recommend.
- Guacamole
- Black beans
- Simple leafy green side salad with a light vinaigrette

Tips From The Nutritionist
Autumn Bates, CCN, MS, BS, CPT
Don’t be scared of corn tortillas! By only using 1-2 small corn tortillas paired with quality protein and veggies, we’re able to enjoy the traditional enchilada experience without a huge spike in blood sugar.
FAQ’s
The ingredients used in classic enchiladas are actually super healthy. Enchilada sauce is made from dried chilis, spices, tomato paste, and broth, which makes it flavorful and nourishing. The rest of the ingredients in this recipe are loaded with protein, micronutrients, and some fiber to keep you satisfied and feeling good.
This recipe was specifically designed to support natural, sustainable fat loss without having to count calories. Because of the high protein content and low glycemic ingredients, this meal can make you feel full and satisfied, which makes weight loss a lot easier.
Other Recipes You May Love
- The Best Low Carb Zucchini Lasagna; This recipe is so good, you won’t even miss the pasta.
- The Best Healthy Shepherd’s Pie; This classic, warming recipe is perfect for weight loss goals!
- Loaded Cheesy Cauliflower Nachos; Everything you love about nachos, without the chips!
Did you love this recipe? Let me know in the comments below!

Healthy Chicken Enchiladas
Ingredients
- 2 teaspoons olive oil
- 2 medium zucchini diced
- 1/2 medium yellow onion diced
- 3 cloves garlic minced
- salt
- 3 cups rotisserie or pre-cooked chicken breast shredded
- 1 jalapeño diced
- 1 tablespoon dried oregano
- 1 teaspoon ground cumin
- 1 teaspoon garlic powder
- 1 teaspoon onion powder
- 1 teaspoon paprika
- 2 1/4 cups red enchilada sauce
- 3/4 cups Mexican-style shredded cheese
- 8 6-inch corn tortillas
Instructions
- Preheat the oven to 400°F. Have on hand four individual-sized ceramic or glass baking dishes, about 5 by 7 inches each.
- Heat the olive oil in a medium-sized skillet over medium heat. Add the zucchini, bell pepper, onion, garlic, and a heavy pinch of salt. Sauté for 5 minutes, or until the veggies have softened.
- Add the chicken, jalapeño, oregano, cumin, garlic powder, onion powder, paprika, and ¼ cup of the enchilada sauce. Stir to combine and cook for 5 to 7 minutes, until all of the ingredients are warmed through. Sprinkle with ¼ cup of the cheese and stir until evenly distributed.
- Spread ¼ cup of the enchilada sauce in each baking dish. Spoon one-quarter of the cooked chicken and veggie mixture into each dish. Top the chicken layer with two tortillas each, overlapping them slightly. Finally, top the tortillas in each dish with another ¼ cup of enchilada sauce and 2 tablespoons of cheese.
- Bake for 15 minutes, or until the cheese is melted and slightly bubbled. Allow to cool for 5 to 10 minutes before serving.
Notes
Equipment
Nutrition
Did you try this recipe?
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