Regulation (EU) 2016/429 introduces comprehensive guidelines for managing transmissible animal diseases, including zoonoses. The subsequent Commission Implementing Regulation 2018/1882 categorizes these diseases into five groups, each with specific responses, ranging from mandatory eradication to optional eradication or surveillance. Key regulatory priorities include enhanced animal traceability, biosecurity, wildlife pathogen control, sustainable farming practices, and minimizing the impact of diseases on public health, animal health, and the environment. These objectives align with the European Green Deal, the Farm to Fork Strategy, the One Health approach, and the ongoing revaluation of European Inner Areas. They, including the Molise Region in Italy, are often remote, face service accessibility challenges, and suffer from depopulation and farm abandonment. Nonetheless, they hold significant potential for agropastoral and agri-food activities that can support tourism, the commercialization of local products, and recreational pursuits. Implementing optional programmes for animal diseases and zoonoses not subject to mandatory eradication could help the farms of these areas to mitigate productivity losses due to diseases like Infectious Bovine Rhinotracheitis and Paratuberculosis. The latter is a suspected zoonosis potentially linked to Crohn’s disease in humans. Optional programmes could enhance economic returns, counteract depopulation, support animal welfare and pasture conservation, and reduce the risk of exposure to zoonotic diseases for residents and tourists attracted by the ecological appeal of these areas.