Prep the marinade: In a bowl, whisk together lime zest, lime juice, minced garlic, olive oil, honey, cumin, smoked paprika, chili flakes (if using), salt, and pepper.
Pat dry the chicken: Use paper towels to dry the chicken thighs. This helps the skin crisp up in the pan.
Marinate: Add the chicken to a large zip-top bag or bowl.
Pour in the marinade and toss to coat. Let it rest for at least 20–30 minutes at room temperature or up to 12 hours in the fridge.
Preheat: Heat the oven to 400°F (200°C). Place an oven-safe skillet (cast iron works great) over medium-high heat with a light drizzle of oil.
Sear skin-side down: Remove chicken from the marinade, letting excess drip off.
Place thighs skin-side down in the hot pan. Sear without moving for 4–5 minutes until the skin is golden and crisp.
Flip and add marinade: Flip the thighs. Pour any remaining marinade into the pan around (not on top of) the chicken.
Roast: Transfer the skillet to the oven and cook for 15–20 minutes, or until the thickest part reaches 165°F (74°C).
Baste once with pan juices halfway through for extra flavor.
Rest and serve: Remove from the oven and let the chicken rest 5 minutes. Spoon pan juices over the top, garnish with chopped herbs, and serve with lime wedges.