Ghana's banking sector and financial services, in general, have seen major significant technological. The implementation of e-ZWICH in Ghana in 2008 was welcomed with great enthusiasm as exciting news that would help the country transition to a cashless economy. Many Ghanaians signed up for the e-ZWICH, the first biometric payment system. After several years, it appears that interest and patronage have declined dramatically. The study investigated challenges and customer perception on E-zwich patronage in Rural Banks. The purpose of the study is to investigate the adoption and sustainability of E-Zwich service in Ghana. To achieve the purpose of the study a descriptive research design was adopted, using the quantitative approach and the administration of questionnaires to 349 respondents in the data collection process using convenience sampling. In this research, Statistical Package for Social Sciences (SPSS) was employed, whereas Structural Equation Modelling (SEM) technique using smart Partial Least Square (PLS) software version 3.0 was also employed. Two assumptions were made by way of hypotheses. The findings of the study revealed that in the comparison of patronage of Ezwich have positive impact on customer perception and E-zwich challenges. The study finds observed that there is a significant positive relationship between patronage of E-zwich on customer perception and E-zwich of challenges judging from the results of the respondents. The study recommends that, in order to increase patronage of e-ZWICH, GhIPSS should intensify their education on how to operate the stand-alone machine. Measures such as sensitization workshops should be organized by the GhIPSS to encourage Ghanaian companies and individuals and in particular the rural folks to patronize the service. Banks and other non-bank financial institutions should show interest and take up e-ZWICH as a core product. Financial institutions should step-up their customer relations in order to motivate and encourage current customers to continue to patronize the service.