Manufacturing has to cope with the continuously increasing variety of products, change of volumes and shortening product life cycles. These trends also affect the automotive sector: the frequent introduction of new models, materials and assembly technologies put the suppliers of make-to-order parts under pressure. In this context, the design of assembly systems and their management are of paramount importance for the companies’ competitiveness. In this paper, we propose an approach for the design and reconfiguration of modular assembly systems through the integration of different computational tools addressing the design of the system, the optimization of the layout, the planning of reconfiguration actions as well as production planning. Integrating these computational tools and iterating through the resulting workflow and feedback allow to consider the outcomes and dependencies of alternative decision sequences holistically with the objective of an effective and efficient approach to production system design and management. The viability of the approach is demonstrated through the application to an automotive case study. © 2017 Elsevier Ltd