This article aims at elucidating the human rights of conscientious objectors to military service and offers detailed substantive guidance for protecting their rights vis-à-vis armed non-State actors and de facto authorities. Persons who live in territory controlled by armed groups or de facto authorities often face human rights protection gaps, for example their freedom of conscientious objection may not be recognized or fully implemented. This article analyzes the practice by international human rights mechanisms in their engagement with de facto authorities in Afghanistan (Taliban), Cyprus (northern part), the Republic of Moldova (Transnistrian region), and Azerbaijan (Nagorno-Karabakh region), along with the related international law on State responsibility and the case-law of the European Court of Human Rights. At the normative level, this article proposes guidelines, following a gradated approach with differentiated obligations based on the capacities of the relevant States, de facto authorities with exclusive control over territory, and armed non-State actors. The article concludes that everyone’s freedom of conscientious objection must be properly protected, irrespective of whether the conscientious objectors happen to live in a territory that is under the control of a State or whether their human rights are negatively affected either through the acts or omissions of a de facto authority or an armed non-State actor.