Escalating intensification and homogenization occurring throughout the supply chain poses serious challenges to the global food supply. Several approaches have been developed to shift the food systems to a more resilient path; however, the high unit costs of shipping impede its development. This paper proposes a shared logistic service supported by E-commerce as a solution to this problem. It analyzes the shared logistic system developed by Vegibus Ins. in Japan which has unique features, such as fixed routes. It argues that the logistic service has the ability to connect different scales while supporting flexible transactions leading to the construction of a resilient agri-food system. At the same time, the paper points out the need for subsidies from the governments to facilitate this kind of shared logistic service at the initial stage as one limitation to this approach.