The coordination of cyclic multi-robot systems is a critical issue to avoid collisions but also to obtain the shortest cycle-time. This paper presents a novel methodology for trajectory and coordination optimisation of cyclic multi-robot systems. Both velocity tuning and time delays are used to coordinate the robots that operate in close proximity and avoid collisions. The novel element is the non-linear programming optimisation model that directly co-adjusts the multi-robot coordination during the trajectory optimisation, which allows optimising these as one problem. The methodology is demonstrated for productivity/smoothness optimisation, and for energy efficiency optimisation. An experimental validation is done for a real-world case study that considers the multi-robot material handling system of a multi-stage tandem press line. The results show that the productivity optimisation with the methodology is competitive compared to previous research and that substantial improvements can be achieved, e.g. up to 50% smoother trajectories and 14% reduction in energy consumption for the same productivity. This paper addresses the current lack of systematic methodologies for generating optimal coordinated trajectories for cyclic multi-robot systems to improve the productivity, smoothness, and energy efficiency.