The agri-food logistics chains face guarantee the greatest extending of sustainability practices in the management of the entire supply chain. The use of management and marketing tools and of innovative legal and economic institutes, also in the agri-food sector, is fundamental to guaranteeing an increasingly “cleaner” agriculture, in order to introduce more and more organic and eco-sustainable food products and safe for the health and well-being of living beings on the market. However, the joint use of these tools does not yet seem to be fully exploited, particularly in South-Italy. In this sense, the territories limit of potential eco-sustainable development tools deriving from the agri-food logistics chains, also in terms of territorial and tourism development of entire areas. Drawing upon the experiences of innovative projects oriented to eco-sustainability that have implemented mechanisms of continuous improvement in the agri-food sector, through the achievement of high levels of technological, methodological and organizational innovation, some implications for how to implement territorial development policies guided by sustainability can be found. In this paper, the changes that the agri-food sector has undergone will be discussed and possible scenarios of territorial and tourism development supported by the agri-food logistics chains will be suggested, two macro areas covered by the three pillars of sustainability, environmental, economic and social.