Automotive suppliers are facing the challenge of continuously adapting their production targets to variable demand requirements due to the frequent introduction of new model variants, materials and assembly technologies. In this context, the profitable management of the product, process and system co-evolution is of paramount importance for the company competitiveness. In this paper, a methodology for the design and reconfiguration management of modular assembly systems is proposed. It addresses the selection of the technological modules, their integration in the assembly cell, and the reconfiguration policies to handle volume and lot size variability. The results are demonstrated in a real automotive case study. © 2016 CIRP