The advent of modern technology in agriculture has increased the efficiency of our food production but also poses pressures on the sustainability of our planet. The Globally Important Agricultural Heritage Systems (GIAHS) of the Food and Agriculture Organization of the United Nations (FAO) has been developed to safeguard traditional agricultural systems of global importance, which harnesses the harmonious relationship between people and nature. First launched in the World Summit on Sustainable Development in 2002 to address the sustainable development of family agriculture and traditional farming practices for developing countries, it now has 59 sites located in 22 different countries as of March 2020. Despite almost two decades of its implementation, FAO has not set any requirements nor given guidance on monitoring of the conservation of GIAHS, but leaves it to the discretion of each GIAHS site to conduct voluntary self-evaluation. This study is a comprehensive review of all 11 GIAHS application proposals in Japan, which aims to (1) conduct characteristic analysis to identify elements and perspectives related to the GIAHS selection criteria, (2) understand the motivations and socioeconomic conditions, including challenges and opportunities related to the GIAHS application, so as to (3) propose a set of indicators and perspectives to address these challenges and opportunities for improving the application, monitoring, and management of the GIAHS. The study finds that motivations for applying to GIAHS designation are primarily driven by push factors of abandonment of traditional farming practices and farmlands and underuse of farming resources resulting from Japan’s decreasing and aging rural population, as well as the pull factor of biodiversity conservation. The importance of continuing traditional farming practices, cultural heritage, and involvement of various stakeholders is emphasized against the background of an aging farming population, rural-urban migration, youth exodus, poor maintenance of farmlands, and transferring traditional and local knowledge. By identifying the drivers of change and understanding the current socioeconomic conditions of the agricultural heritage systems in Japan as portrayed in the GIAHS application proposals, the study has clarified the strengths and challenges of the sustainability of these systems. Based on the analysis, the study proposes a comprehensive set of indicators to be considered when developing the GIAHS proposals and for updating the action plan for monitoring and managing the GIAHS sites. It is expected that the findings and recommended indicators will contribute not only to the improvement of the information integrity of future GIAHS proposals but also as a reference for the development and monitoring of GIAHS conservation action plans.