In France, as in numerous countries, healthcare organisations are undergoing major transformations, leading them to rationalise their resources and optimize their flows. In this context, automation can play an important role, enabling value creation and patient satisfaction. Previous research has mainly focused on the technological aspects of automation, neglecting the organisational issues related to the implementation of this innovation and particularly the management of the hospital staff, including logistics personnel, involved within the organisational change process. The aim of this article is, at least, to partly address this gap within the literature, and to propose, based on an exploratory case study, an analysis grid of the challenges and changes in terms of logistics flows (pharmaceutical, waste, laundry, etc.) that impact staff involved in managing these flows in a hospital context. Our results highlight the importance and necessity of anticipating the building and deployment of new knowledge and skills in order to efficiently and effectively design and manage automated logistics flows with AGV system.