Agricultural collapse in conflict-affected states is often attributed to environmental stress or technical failure, yet in South Sudan it reflects deeper political and institutional processes. Successive cycles of conflict, displacement, and aid dependence have systematically dismantled rural livelihoods and productive systems. This study examines how politically produced agricultural decline shapes political order from the liberation period to the present, with comparative reference to Mozambique and Rwanda. Drawing on agrarian political economy, food sovereignty, livelihoods analysis, and the conflict–agriculture nexus, the study combines longitudinal analysis of agricultural and food security data with political economy fieldwork, interviews with farmers and officials, and cross-case comparison. The findings show that agricultural collapse is not a short-term crisis but a durable outcome of institutional and political dynamics that reshape incentives, authority, and access to land, labour, and markets over time (Bernstein 2010; McMichael 2013; Scott 1976; Chambers & Conway 1992). Conflict-driven displacement, weakened governance, and reliance on humanitarian systems disrupt production while reinforcing dependency. Variation across cases highlights the importance of political settlement, land governance, and state support in enabling recovery. The contribution lies in linking agricultural decline to the broader political economy of conflict, demonstrating that rebuilding rural livelihoods requires more than technical intervention. Durable recovery depends on institutional reform, political bargaining, and accountability mechanisms that address the underlying distribution of power (DFID 1999; FAO 2023; WFP 2024; de Waal 1997).