States must investigate possible violations of international humanitarian law in armed conflict, and many States use military procedures for all or part of the investigation process. Particular tensions can arise with regard to the perception of justice in the context of military judicial procedures, especially surrounding questions of independence and impartiality. This article lays out the international legal framework which should be used to solve these challenges, arguing that a State must address both the specificities of military institutions and the need for a perception of justice by the affected communities in considering the proper administration of justice in armed conflict.