There is a remarkable discrepancy between the political representation of the Batwa ethnic minority group in Burundi compared to in Rwanda. Whereas Rwanda’s focus on citizenship prevents the Batwa from claiming recognition as a politically salient societal segment, Burundi’s governance model, characterized by ethnic, consociational power-sharing, guarantees the political representation of the Batwa in the legislative assemblies. The difference is mainly due to the various modalities of political transition that both countries have experienced. While in Rwanda, regime change came about through a military victory, Burundi’s transition from conflict to peace involved a long and complex peace-negotiations process, with international mediators viewing the armed conflict and its resolution in explicitly ethnic terms. The Arusha Peace and Reconciliation Agreement was a foundational moment for the recognition of the political participation rights of the Batwa in Burundi, despite the fact that they were not actively involved in Burundi’s armed conflict, or in the peace negotiations. The comparative analysis in this paper offers insights into the potential of peace processes with respect to improved minority-rights protection following violent conflict.