Information system implementation helps to promote efficiency of the workshops and enterprises’ competitiveness. It requires holistic analyses and investigation in the manufacturing workshops to ensure its success. This research proposes a framework to guide information systems implementation in discrete manufacturing workshops. In the framework, multi-agent simulation models are built to analyze the business processes in the workshops and some techniques from Business Process Management (BPM) are applied to modify or change the processes. The effectiveness of the framework is proved by its application in a discrete manufacturing workshop.