Biodiversity and ecosystem conservation in the Amazon play a critical role in climate-change mitigation. However, institutional responses have had conflicted and complex relations with Indigenous peoples. There is a growing need for meaningful engagement with—and recognition of—the centrality of Indigenous peoples’ perceptions and understanding of the changes they are experiencing to inform successful and effective place-based adaptation strategies. To fill this gap, this study focuses on the value-based perspectives and pragmatic decision-making of Shawi Indigenous men in the Peruvian Amazon. We are specifically interested in their perceptions of how their food system is changing, why it is changing, its consequences, and how/whether they are coping with and responding to this change. Our results highlight that Shawi men’s agency and conscious envisioning of their future food system intersect with the effects of government policy. Shawi men perceive that the main driver of their food-system changes, i.e., less forest food, is self-driven population growth, leading to emotions of guilt and shame. During our study, they articulated a conscious belief that future generations must transition from forest-based to agricultural foods, emphasising education as central to this transition. Additionally, results suggest that the Peruvian government is indirectly promoting Shawi population growth through policies linking population size to improved service delivery, particularly education. Despite intentional Shawi moves to transition to agriculture, this results in a loss of men’s cultural identity and has mental-health implications, creating new vulnerabilities due to increasing climatic extremes, such as flooding and higher temperatures.