The Portuguese footwear industry registered a strong performance over the last few years and the openness to adopt new technologies was a key factor. Among these, the implementation of innovative logistic systems for the transport and assignment of work-in-process in manufacturing processes was a key technology. By means of case research it was analyzed an internal logistic system, deployed in a Portuguese large footwear producer, which reveals some weaknesses at the physical and cyber levels. A lack of managing applications was detected at the factory and enterprise levels, which contribute to lower levels of visibility of production and productivity. This article presents the development of a Cyber-Physical Production System, in the context of the Horizon 2020 research and innovation program BEinCPPS, that comprises four application experiments. These experiments were successful and the results demonstrated a relevant increase of production efficiency and decrease of maintenance costs.