For some years now, the automotive industry has been challenged by growing market dynamics, shorter product lifecycles and customers' increasing demands for individualization. In order to cope with this development, the automotive assembly needs to adapt quickly to changing demands with a low level of investment in the future. Under the current circumstances, the traditional line assembly for high volume production is reaching its limits in terms of adaptability and scalability. A promising solution to address the current challenges is the concept of the agile assembly. The concept of agile assembly breaks up the rigid linkage of assembly stations and, thus, enables full flexibility in the sequence of assembly operations only limited by the precedence graph. Therefore, the routing of electric vehicles in the agile assembly is based on the availability of resources such as assembly stations and automated guided vehicles that handle the material supply. Further, by transferring the transport function to the vehicle itself, investments for convey or systems are eliminated. This research work presents an optimization approach for the machine scheduling and transportation planning, which derives instructions for electric vehicles, assembly stations as well as automated guided vehicles. For each electric vehicle, an optimized route is calculated, taking into account product-specific precedence graphs and minimizing the overall makespan. In addition, the machine scheduling and transportation planning is integrated into a combined planning and control concept which covers the allocation of resources and the assignment of capabilities of the entire assembly system. The approach is implemented and applied to a practical case of a compact electric vehicle. Thus, the work contributes to the evaluation of agile assembly systems in automotive production.