Make the sauce: In a bowl or large measuring cup, whisk together shoyu, water, brown sugar, garlic, ginger, rice vinegar, honey, sesame oil, black pepper, and red pepper flakes if using. Stir until the sugar dissolves.
Prep the chicken: Pat the chicken thighs dry with paper towels.
This helps the skin brown lightly and keeps the sauce from getting watery.
Sear for extra flavor (optional but recommended): Heat a large pot or Dutch oven over medium-high heat. Add a splash of neutral oil. Place chicken skin-side down and sear for 3–4 minutes until lightly golden.
Flip and sear 2 minutes more. Work in batches if needed. Remove excess fat if there’s a lot.
Add the sauce: Pour the sauce into the pot with the chicken.
The liquid should come about halfway up the pieces. If needed, add a splash more water.
Braise gently: Bring to a gentle boil, then reduce heat to low. Cover and simmer for 25–30 minutes, turning the chicken once halfway through.
The chicken should be tender and cooked through.
Reduce the sauce: Remove the lid and simmer another 10–12 minutes to concentrate the flavors. Spoon sauce over the chicken as it thickens. You’re looking for a glossy, slightly syrupy consistency that coats a spoon.
Adjust to taste: Taste the sauce.
If it’s too salty, add a splash of water or a touch more honey. If too sweet, add a dash more soy sauce or vinegar.
Serve: Transfer the chicken to plates or a serving platter. Spoon plenty of sauce over the top.
Garnish with green onions and sesame seeds. Serve with hot rice and your favorite sides.