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Civil wars are the primary source of contemporary violent conflict worldwide, resulting political instability, economic losses, social fragmentation, and death. However, not all legacies of civil wars are negative. This paper explores the role of militias (counterinsurgency or self-defense groups) in post-conflict scenarios to answer the following: Under what conditions can militia organizations persist and improve rural governance? Drawing from immersive fieldwork in rural Peru, I propose a novel theoretical framework for understanding militias’ post-conflict paths. I argue that these paths depend on militias’ wartime relationships with the state (the Armed Forces) and the local community. Militias that operate with a high degree of autonomy from the Armed Forces and protect the local community during the conflict are more likely to endure and contribute to rural governance after civil wars. Conversely, militias that are subjugated to the Armed Forces and prey on the local community are less likely to survive in post-conflict periods. Site-intensive methods, including interviews, archival sources, and participant observation, support a qualitative cross-case comparison of two subnational cases within Peru. The paper sheds light on the unintended positive legacies of violent conflict and underscores the importance of considering militia governance alongside other forms of non-state governance, such as rebel governance and chieftaincy institutions.