Over the last decades, anti-corruption agencies have become widely adopted in states emerging from violent conflict. A particularly relevant rationale for the establishment of anti-corruption agencies in contexts of weak governance is their potential to improve the legitimacy of the state by showing the government’s commitment to counter corruption. Yet a conceptual framework to explain the effect of anti-corruption agencies on state legitimacy is missing and no comparative research has been done to gauge this effect. This article argues that the institutional design of anti-corruption agencies influences but does not determine the effect on state legitimacy. Effective anti-corruption agencies – which literature suggests to depend on their political independence, resources and powers, jurisdiction and transparency mechanisms – have the potential to improve state legitimacy. However, this effect is contingent on the continued support anti-corruption agencies receive from the government, the expectations and track record of results from anti-corruption cases investigated by the agencies and finally their ascription to the state. The article first summarises the theoretical expectations about the effect of anti-corruption agencies on the legitimacy of governments and state institutions in fragile and conflict-affected contexts. Then, this relationship is comparatively assessed based on an index measuring the institutional capacities of anti-corruption agencies. Finally, these results are discussed by drawing further insights from an in depth case study, Nepal's Commission for the Investigation of the Abuse of Authority.