Armed conflict in South Sudan has not simply eroded customary governance; it has reconfigured it. Chiefs and elders have increasingly become brokers of security, aid, mobility, and legitimacy, operating within a landscape where authority is expanded, politicised, and contested. The concept of militarised customary brokerage captures how customary institutions are reshaped under conditions of sustained violence, transforming their roles within systems of legal pluralism and local governance. Situated within debates on African political order, state formation, and institutional design, the manuscript examines how conflict restructures rather than destroys traditional authority. Focusing on South Sudan, with comparative reference to Northern Uganda and Eastern Democratic Republic of the Congo, the study addresses three interrelated questions: how prolonged conflict has reshaped the authority, legitimacy, and political economy of chiefs and elders in Dinka, Nuer, and Acholi communities; under what conditions armed groups co-opt customary authorities as recruitment brokers, tax intermediaries, and intelligence sources, and how this affects their legitimacy; and what role customary dispute resolution practices—such as cattle compensation, inter-clan negotiation, and Mato oput—play in community-level conflict management, particularly in relation to formal transitional justice processes. Methodologically, the study draws on multi-site ethnographic fieldwork in Bor, Rumbek, Torit, and Yambio, complemented by interviews with chiefs, women’s groups, youth leaders, and returned internally displaced persons. It also incorporates archival research in Church of Sudan and colonial administrative records, alongside comparative analysis with Northern Uganda and Eastern DRC. The findings