Make the marinade: In a bowl, mix lime zest, lime juice, olive oil, garlic, cilantro, honey, cumin, salt, pepper, and chili flakes (if using). Reserve 2 tablespoons in a small container for serving.
Prep the chicken: Pat the thighs dry with paper towels. This helps them sear well and not steam in the pan.
Marinate: Add the chicken to the marinade and toss to coat.
Cover and marinate in the fridge for at least 20–30 minutes, up to 8 hours. The lime keeps it bright, but don’t go past 12 hours or it can get mushy.
Choose your cooking method: For the stovetop, use a large skillet or cast-iron pan. For grilling, preheat to medium-high.
For the oven, set to 425°F (220°C).
Cook on the stovetop: Heat 1 tablespoon oil in a skillet over medium-high. Shake excess marinade off and sear thighs 5–6 minutes per side, until deeply browned and the internal temperature reaches 165°F (74°C).
Or grill: Oil the grates. Grill thighs 5–6 minutes per side over direct heat, flipping once.
Move to indirect heat if they’re browning too fast.
Or roast: Arrange thighs on a lined sheet. Roast 18–22 minutes, broiling for the last 2 minutes for extra color if desired.
Rest and finish: Let the chicken rest 5 minutes. Spoon the reserved marinade over the top, then squeeze more lime if you like.
Serve: Plate with cilantro-lime rice, roasted corn, avocado, and warm tortillas.
Add a dollop of yogurt or crema to cool the heat.