People in the department of Madre de Dios/Peru, the state of Acre/Brazil, and the department of Pando/Bolivia experience similar conflicts over land, land use, and access to resources. At the same time, each conflict reveals distinct characteristics and dynamics, arising from its history, legal regulation, institutional (in-)capacities, and culturally diverse local populations. The aim of this paper is to better understand the main drivers of social-ecological conflicts over land in and around three protected areas in this transboundary region, known as MAP, and to analyze how (environmental) institutions influence these drivers. The paper is based on a literature review and expert interviews; it focuses on conflicts around (1) gold mining in Madre de Dios, (2) extensive cattle ranching in Acre, and (3) access to communal land in Pando. Using theories of conflict research, expanded by a political ecology perspective and insights from stakeholder and expert interviews, we find that the major conflict drivers are (1) land tenure and access to land and natural resources, (2) identity and lifestyle driven transformations, (3) state and market driven agendas, and (4) networked illegal and criminal activities. Through a comparative conflict analysis, we develop four recommendations to strengthen the creation of reflexive institutions that may be able to foster social-ecological resilience in the region: (1) The clarification of responsibilities between governance institutions and their financing; (2) the awareness raising for existing power structures and opening spaces for enhanced local participation; (3) the breaking of corruptive cycles while developing economically, ecologically, and socially sustainable livelihood opportunities; and (4) taking the continuous reproduction of illegal activities into account while clarifying responsibilities, raising awareness, and breaking corruptive cycles. The results of our research therefore not only contribute to a better understanding of conflicts in the MAP region and the wider scientific literature on social-ecological conflicts and governance, but it is also the first paper that identifies entry points and prerequisites for the transformation from reactive to reflexive institutions in Amazonian societies.