Reconfigurable manufacturing systems (RMS) intend to bridge the gap between dedicated and flexible manufacturing systems. If the literature is mainly focused on the design step and tactical planning of such systems, few research projects have addressed scheduling at the operational level. While setup times may occur in flexible manufacturing systems, reconfiguration times considered in RMS may affect several resources at once, and hence require specific modelling and solving approaches to be considered. This paper first formalises the problem at hand through integer linear programming. An iterative search method is then provided to obtain solutions to larger-scale instances. Results obtained on generated instances show that managing even few possible configurations can yield significant improvements in solutions’ quality. Meanwhile, the extended search space implied by the increase in available configurations hinders the convergence to a good solution in a reasonable computation time, which suggests further investigations.