Information systems leave a traceable digital footprint whenever an action is executed. Business process modelers capture these digital traces to understand the behavior of a system, and to extract actual run-time models of those business processes. Despite the omnipresence of such traces, most organizations face substantial differences between the process specifications and the actual run-time behavior. Analyzing and implementing the results of systems that model business processes tend, however, to be difficult due to the inherent complexity of the models. Moreover, the observed reality in the form of lower-level real-time events, as recorded in event logs, is seldom solely explainable by higher-level process models. In this paper, we propose an architecture to model systemwide behavior by combining process mining with a multi-agent system. Digital traces, in the form of event logs, are used to iteratively mine process models from which agents can learn. The approach is initially applied to a case study of a simplified job-shop factory in which automated guided vehicles (AGVs) carry out transportation tasks. Numerical experiments show that the workflow of a process mining model can be used to enhance the agent-based system, particularly, in analyzing bottlenecks and improving decision-making.