As the first biometric payment system in Africa, the e-ZWICH payment system was meant to facilitate trade and simplify payments, which will then drive economic growth and development. This novel payment system has been bedeviled with a lot of challenges. Various studies have been conducted into challenges of e-ZWICH payment systems in Commercial Banks with little or no special attention to small and medium scale enterprise. This study was therefore initiated to investigate challenges of e-ZWICH payment system on small and medium scale enterprises and find out if significant differences existed on perceived challenges of e-ZWICH payment system according to customersâ€™ geographical zones. This study will lead to an improvement in the use of e-payments systems by small and medium scale enterprises.