In a large bowl, combine apple juice, lime zest, salt, and pepper. Cut chicken breasts in half and add to bowl, turning to ensure they are coated.
Cover bowl and place in refrigerator to marinate for 30 minutes.
Meanwhile, combine apples, pepper flakes, onion, and lime juice in a small bowl. Add salt and pepper to taste.
Remove chicken from the fridge and drain marinade. Cook chicken with your preferred cooking method, ensuring it reaches an internal temperature of at least 165 degrees F.
Serve topped with crunchy apple salsa. Store leftovers in fridge within two hours and eat within four days.