Urgent challenges posed by widespread degradation in tropical ecosystems with poor governance require new development pathways to reconcile biodiversity conservation and human welfare. Community-based conservation management has shown potential for integrating socio-economic needs with conservation goals in tropical environments; however, assessing the effectiveness of this approach is often held back by the lack of comprehensive ecological assessments. We conduct a robust ecological evaluation of the largest community-based conservation management initiative in the Brazilian Amazon over the last 40 years. We show that this programme has induced large-scale population recovery of the target giant South American turtle (Podocnemis expansa) and other freshwater turtles along a 1,500-km section of a major tributary of the Amazon River. Poaching activity on protected beaches was around 2% compared to 99% on unprotected beaches. We also find positive demographic co-benefits across a wide range of non-target vertebrate and invertebrate taxa. As a result, beaches protected by local communities represent islands of high biodiversity, while unprotected beaches remain ‘empty and silent’, showing the effectiveness of empowering local conservation action, particularly in countries experiencing shortages in financial and human resources.