If you're craving classic comfort food without the carb overload, these low carb chicken enchiladas are the perfect solution. Made with almond flour tortillas, lean shredded chicken, and a creamy high-protein filling.
This healthier enchilada recipe delivers bold flavor while keeping carbs in check. It's everything you love about traditional enchiladas - just lighter, cleaner, and better for everyday eating.
Unlike restaurant-style enchiladas that rely on refined flour tortillas and heavy cheese, this recipe focuses on protein-forward ingredients like chicken breast, cream cheese, and reduced-fat cheese.
The result is a satisfying, gluten-free meal that works beautifully for low-carb, keto-adjacent, and high-protein lifestyles.
Jump to:
- Why You'll Love These Low Carb Chicken Enchiladas
- Ingredients You'll Need
- How to Make Low Carb Chicken Enchiladas
- Tips for Perfect Low Carb Enchiladas
- Variations and Substitutions
- Make Ahead, Storage, and Reheating
- Are Chicken Enchiladas Low Carb?
- What to Serve with Low Carb Chicken Enchiladas
- Low Carb Chicken Enchiladas (High Protein & Gluten-Free)
Why You'll Love These Low Carb Chicken Enchiladas
- High in protein and naturally low in carbs
- Made with almond flour tortillas instead of corn or flour
- Gluten-free and meal-prep friendly
- Creamy, cheesy, and full of enchilada flavor
- Easy to customize with veggies or spice
Ingredients You'll Need
This low carb chicken enchilada recipe uses simple, easy-to-find ingredients:
- Cooked shredded chicken breast (or rotisserie chicken)
- Almond flour tortillas (6-7 inch)
- enchilada sauce (red or green)
- Reduced-fat shredded cheese and cream cheese
- Greek yogurt for extra protein (optional)
- Onion, garlic, and warm spices like cumin and chili powder
Using almond flour tortillas keeps the dish gluten-free and significantly lower in carbs, while Greek yogurt replaces heavy cream or sour cream without sacrificing the flavor.
How to Make Low Carb Chicken Enchiladas
- Prepare the filling: Sauté onion and garlic, then mix with shredded chicken, spices, cream cheese, and enchilada sauce.
- Warm the tortillas: Briefly heat almond flour tortillas so they're flexible and easy to roll.
- Assemble: Fill each tortilla with the chicken mixture, roll tightly, and place seam-side down in a baking dish.
- Top and bake: Pour enchilada sauce over the top, sprinkle with cheese, and bake until bubbly and lightly golden.
- Rest and serve: Let the enchiladas rest for a few minutes before serving for best texture.
Tips for Perfect Low Carb Enchiladas
- Warm tortillas before rolling to prevent cracking.
- Use thick enchilada sauce to avoid sogginess.
- Don't overfill, almond flour tortillas are more delicate.
- Let enchiladas rest after baking so they hold together better.
Variations and Substitutions
- Extra high protein: Add blended cottage cheese to the filling.
- Spicy version: Use pepper jack cheese or add diced jalapeños.
- Green enchiladas: Swap red sauce for green enchilada sauce.
- Veggie-packed: Add spinach, zucchini, or cauliflower rice (pre-cooked).
- Casserole-style: Layer tortillas and filling instead of rolling.
Make Ahead, Storage, and Reheating
These low carb chicken enchiladas are ideal for meal prep.
- Make ahead: Assemble up to 24 hours in advance and refrigerate.
- Store: Keep leftovers in an airtight container for up to 4 days.
- Freeze: Freeze baked or unbaked enchiladas for up to 2 months.
- Reheat: Warm in the oven at 350°F or microwave until heated through.
Are Chicken Enchiladas Low Carb?
Traditional chicken enchiladas are not low carb due to flour or corn tortillas. However, using almond flour tortillas makes this recipe significantly lower in carbs while still delivering the same comforting flavors.
What to Serve with Low Carb Chicken Enchiladas
- Mango Salsa
- Instant Pot Cilantro Lime Rice
- Mexican-style zucchini sauté
- Instant Pot Refried Beans (vegan, gluten-free)
- Avocado slices or guacamole
- Simple cabbage slaw
These low carb chicken enchiladas prove that comfort food can absolutely fit into a healthy lifestyle. With high protein, fewer carbs, and tons of flavor, this recipe is perfect for weeknight dinners, meal prep, or when you're craving enchiladas without the guilt.
Once you try them, they're sure to become a regular in your healthy dinner rotation.
Low Carb Chicken Enchiladas (High Protein & Gluten-Free)
Equipment
- 1 Skillet
Ingredients
For the Chicken Filling
- 1 lb cooked chicken breast ,shredded (rotisserie or poached)
- 1 teaspoon olive oil
- ½ small onion ,finely diced
- 1 jalapeno ,de-seeded, finely chopped (optional)
- 2 cloves garlic ,minced
- 1 teaspoon ground cumin
- 1 teaspoon chili powder
- ½ teaspoon smoked paprika
- ½ teaspoon dried oregano
- Salt & black pepper ,to taste
- ¼ cup low-carb enchilada sauce ,or sugar-free store-bought
For the Enchiladas
- 6 almond flour tortillas (6-7 inch)
- ¾ cup low-carb enchilada sauce ,divided
- 1 cup reduced-fat shredded Mexican blend cheese ,or part-skim mozzarella + cheddar mix; plus more for the topping
- 2 tablespoon fat free cream cheese
- ¼ cup chopped bell peppers or zucchini optional
For Greek Yogurt Sauce: (optional, replace sour cream)
- ¼ cup Greek Yogurt ,blended smooth
- 1 lime juice , to taste
- salt to taste
Toppings (optional):
- Fresh cilantro ,pickled jalapeno, or green onions
Instructions
- Preheat oven to 375°F (190°C). Lightly grease a small baking dish (8×8 works great).
Make the filling:
- Heat olive oil in a skillet over medium heat. Sauté onion for 2–3 minutes until soft. Add garlic and cook 30 seconds.
- Stir in cumin, chili powder, paprika, oregano, salt, and pepper. Add shredded chicken and mix well.
- Turn heat to low. Stir in cream cheese and ¼ cup enchilada sauce until creamy. Remove from heat.
Assemble the Enchiladas:
- Warm almond flour tortillas slightly on a skillet (or microwave 10-15 seconds so they don't crack).
- Lightly grease a baking dish and spread a thin layer of enchilada sauce on the bottom.
- Lay one almond flour tortilla flat, spread 1-2 tablespoons of enchilada sauce evenly over the tortilla.
- Fill each tortilla with about ⅓ cup chicken mixture, sprinkle with a little cheese, roll tightly, and place seam-side down in the dish.
Bake:
- Pour remaining ½ cup enchilada sauce over the tortillas. Sprinkle evenly with remaining cheese.
- Bake uncovered for 18-22 minutes, until bubbly and lightly golden.
- Rest 5 minutes, then garnish with cilantro, green onions, or a dollop of Greek yogurt sauce.
- (Optional) In a small bowl, whisk together Greek yogurt, fresh lime juice, and a pinch of salt until smooth and creamy. Use this mixture in place of sour cream and serve alongside the enchiladas.
Notes
- Sour Cream Substitute: Greek yogurt mixed with lime juice and salt gives the same tangy, creamy finish with extra protein and fewer carbs.
- Chicken Options: Use rotisserie chicken breast, leftover grilled chicken, or shredded chicken.
- Tortillas: Warm almond flour tortillas slightly before filling to prevent cracking.
- Cheese: Reduced-fat cheese keeps the dish lighter, but full-fat works if preferred.
- Make It Spicy: Add chopped jalapenos or a pinch of cayenne to the chicken mixture.
- Serving Tip: Serve with extra yogurt-lime sauce and pico-de-gallo on the side.
Nutrition
Disclaimer
Nutrition values are my best estimates. If you rely on them for your diet, use your preferred nutrition calculator.
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