In a medium bowl, whisk together honey, lime juice and zest, garlic, olive oil, soy sauce, and chili flakes. Taste and adjust seasoning as needed.
Place the chicken thighs in a large zip-top bag or shallow dish. Pour the marinade over the chicken, coating well. Seal and refrigerate for at least 30 minutes or up to 4 hours.
Preheat the oven to 400°F (200°C). Arrange the marinated chicken thighs in a baking dish, skin side up. Spoon extra marinade over the top. Bake for 35–40 minutes, or until the internal temperature reaches 165°F and the skin is golden brown.
Let the chicken rest for 5 minutes before serving. Garnish with fresh cilantro and a squeeze of lime, if desired.