The persistence of indigenous poverty and exclusion is one of the main challenges for social policy in Latin America. Social protection programmes, in particular conditional cash transfers, have been among the main instruments used by governments over the past two decades to respond to the high incidence of poverty in indigenous contexts. The inclusion of indigenous peoples as social protection beneficiaries remains a largely unexplored topic, despite its relevance to understand social policy trajectories in the global South. This article discusses the expansion of poverty alleviation social programmes in the Peruvian Amazon. Although the expansion of these programmes increased the state’s capacity to deliver welfare services in historically excluded areas, it also revealed the limitations of existing social protection instruments to effectively respond to indigenous poverty and vulnerability. Addressing this challenge constitutes a key opportunity to promote transformative approaches in social protection systems in Latin America.