This study aims to provide an integrated methodology for re-designing the layout and departmental organisation in a job shop environment. While several studies have discussed the specific re-design or re-organisation of small- and medium-sized enterprises (SMEs) through simulation or mathematical models performing improvements, an integrated approach is rare. An integrated simulation-based methodology has been developed for simultaneously re-designing the layout and the departmental organisation of an SME manufacturing facility. A wooden chair manufacturing facility has been used as a case study. It is found that the developed methodology might be useful for other SME manufacturing firms, especially in the furniture industry.