Agroecology, as a science, practice, and social movement, has been posed as a potential pathway to revitalize global food systems through a shift towards social and ecological justice. Complex and diversified agroecological systems vary widely globally and have been poorly characterized by traditional agronomic assessments that often focus narrowly on income and yield over other socioecological dimensions such as farmer and worker well-being, dietary diversity, environmental impacts and biodiversity conservation. In response, we propose an approach to the digital monitoring and assessment of agroecological practices that acknowledges and respects diverse contexts and improves power dynamics by centering on the agency and biocultural knowledge of diverse farmers and communities. We describe a community-university partnership designed to develop a farmer-driven, open-access, and open-source digital tool for agroecological monitoring and certification. The farmer-scientist research team aims to chart a course for researchers to investigate how trade-offs among productive, sociocultural, economic, and/or environmental indicators might be minimized to enhance overall system sustainability across diverse contexts globally while also providing tools of use to agroecological farmers and their organizations, who can then autonomously capture (some of) the benefits of the digital agricultural revolution without ceding data sovereignty.