The PEPPERONI consortium has developed a comprehensive concept for the pilot line infrastructure and operation. Previous investments accelerated the early stages of facilitation, which was continued by controlling material flow as well as media and waste management for the respective process steps. Hence, most of the groundwork has been successfully finished and the required workflows for a potential high-throughput operation are established. In conclusion, a concept for high-throughput operation of the pilot line has been developed, which marks a significant milestone toward a goal of pilot fabrication of efficient tandem cells and modules at the end of the project.