This paper analyses direct management of COVID-19 in Brazil, Colombia and Peru, the three largest countries in the Western Amazon region. Using information gathered from different sources and analysing them through comparative case studies and content analysis, this study reveals the scale of disruption endured by Indigenous communities living in the region caused by COVID-19. While findings identify several shortcomings and failures in policies adopted by national and local governments in dealing with the pandemic, they also highlight how some Latin American countries used the crisis to introduce reforms to deepen neoliberal New Public Management (NPM) policies and practices.