Pursuant to the doctrine of command responsibility, military commanders can be found criminally responsible for having failed to take necessary and reasonable measures to prevent or punish the crimes of their subordinates. Focusing on the duty of commanders of organized armed groups to punish the war crimes committed by their subordinates, this article enquires whether the commanders’ duty is subject to any limit under international law. By analysing the imposition of disciplinary and criminal measures, including prosecution in armed group courts and detention, the article argues that a commander cannot fulfil their duty to punish through unlawful measures and can only be required to take punitive measures which are not themselves illegal or criminal under international law. Otherwise, the commander would face a paradoxical choice: not punish their subordinates and be punished for having failed to do so or punish them and nonetheless be punished for having done so through illegal or criminal measures. Courts should be mindful of this when holding an individual responsible for failing to take certain punitive measures pursuant to the doctrine of command responsibility.