Biodiversity protection encompasses key aspects directly related to the sustainability of our food systems: BFA provides a diverse and heterogenous biological basis for diverse and resilient production systems, for the pollination of cultures, for increased diversity of food, and is strongly linked to local and indigenous knowledge on local crops and breeds acknowledged as cultural heritage. This study examines the existence of data collection, monitoring systems, and conservation initiatives as well as legislation and policies related to biodiversity for food and agriculture in the three following regions: (1) Central Asia, (2) the South Caucasus countries, Turkey, Belarus and Ukraine and (3) the Western Balkan countries and the Republic of Moldova. From this study, it appears that none of the three studied regions currently have any solid monitoring schemes for agricultural biodiversity, nor do they have a strong legal framework for protecting farmers’ rights to seeds that would allow them, amongst other things, to maintain biodiversity. Conservation actions, policies, and legislation generally concern wild biodiversity conservation (through habitat protection) and crop genetic resources conservation but rarely address biodiversity for food and agriculture or wild biodiversity loss caused by food systems. The three regional reports conducted in the framework of this study reported a general lack of capacities and a particularly low level of involvement of farmers and other food producers in monitoring, data collection, and conservation activities. The combination of these two major observations leads us to the conclusion that the governance of BFA should be transformed to put food producers at the centre of biodiversity monitoring and conservation, in dialogue with scientists and institutional actors. Their specific expertise must be acknowledged and valued in the efforts of preserving the biodiversity that they cultivate and sustain. Beyond this needed shift in the governance of monitoring activities, we highlight the necessity of a regional articulation of monitoring efforts and a specific focus on local threatened varieties and breeds (beyond habitat conservation), while very comprehensively considering BFA and wild biodiversity impacted by food systems. Regarding biodiversity protection, we recommend – in addition to farmer-centered data collection and monitoring system implementation – addressing the root causes of biodiversity loss, adopting a systematic approach in legislations, policies, and actions while supporting agroecology, and fulfilling international instruments that guarantee the rights of producers to grow and raise local varieties and breeds.