Indigenous communities in the Amazon are facing rapid socio-ecological changes that threaten traditional land management practices and food sovereignty. Indigenous knowledge and practices, essential for biodiversity conservation, are quickly being lost. I examine how changes in traditional land management affect Indigenous food sovereignty and its impact on the growth of women’s leadership in Mitú, Colombia. Through ethnographic fieldwork and using the lens of Feminist Political Ecology, I discuss how structural inequalities, weakened governance, and climate change are significant barriers to Indigenous food sovereignty. There is an increased separation from agricultural spaces, however, women are actively re-signifying these spaces through grassroots leadership. This case study highlights the importance of Indigenous women reclaiming their knowledge and practices as a tool for empowerment and community-centered territorial governance. Recognizing and supporting leadership processes of Indigenous women in food systems is necessary to building resilient, sustainable, and inclusive futures for the Amazon.