Zest the limes before juicing them. Ensure you're only getting the green outer portion, as the white pith can add unwanted bitterness.
In a food processor, combine cilantro, garlic, lime zest, and oil. Pulse 8-10 times until the cilantro is finely chopped but not completely pureed.
Transfer the mixture to a bowl. Whisk in lime juice, honey, salt, cumin, coriander, black pepper, and red pepper flakes (if using) until thoroughly combined.
If using chicken breasts, ensure they are of even thickness (approximately 1-inch) by gently pounding thicker portions. Pat the chicken dry with paper towels to remove excess moisture.
Place chicken in a resealable plastic bag or shallow glass container. Pour marinade over chicken, ensuring all surfaces are coated. Press out excess air if using a bag and seal tightly.
Refrigerate and marinate according to your cut of chicken: boneless breasts (2-4 hours), bone-in breasts (4-6 hours), thighs/legs (4-6 hours), or whole chicken (8-12 hours).
Remove chicken from marinade and pat lightly with paper towels to remove excess surface moisture. This promotes better browning during cooking. Discard used marinade.
Cook as desired: grill, bake, or pan-sear the marinated chicken until it reaches an internal temperature of 165°F (74°C).