Soak wooden skewers in water for 20–30 minutes if using. Preheat grill to medium-high heat.
Whisk pineapple juice, soy sauce, ketchup, brown sugar, rice vinegar, oil, garlic, ginger, pepper, salt, and red pepper flakes in a bowl.
Reserve about 1/4 cup of the mixture for brushing. Toss chicken with the remaining marinade and chill 20–30 minutes.
Oil grill grates. Pat chicken dry. Fold bacon pieces in half so they fit neatly on skewers.
Thread skewers, alternating chicken, folded bacon, pineapple, peppers, and onion. Repeat, ending with pineapple.
Grill kebabs 12–15 minutes, turning every few minutes, until chicken reaches 165°F and bacon crisps.
Brush with the reserved glaze during the last 3–4 minutes for a glossy finish.
Rest 3 minutes. Sprinkle with cilantro and serve hot.