Firms cannot be competitive if their information systems (ISs) and business strategies are not aligned. The strategic alignment model (SAM) developed by Henderson and Venkatraman (Strategic alignment: leveraging information technology (IT) for transforming organizations. IBM Systems Journal, 38 (2/3), 472–484.) considers strategic alignment as a stand-alone challenge between a company and its IS. This concern of alignment has not been empirically extended to the inter-organisational level. This research raises the question of inter-organisational alignment and follows how companies, embedded in a supply chain (SC), adapt their ISs and organisations while implementing IT-driven innovation. We conducted a case study on a radio frequency identification (RFID) project in a jewellery SC. This SC is made of a middle-sized retailer (MSR), composed of headquarters and 80 stores, and one single supplier, a logistic service provider (LSP). By combining an RFID project framework and the SAM, this study provides some answers to the dynamics of alignment and highlights various sequences according to the different phases of the project. Through a single case study, this article finally proposes to extend the alignment perspectives of the SAM to the inter-organisational level.