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E-banking has continuously brought changes on our daily lives by enabling provision of fully automated banking services that do not require visiting a bank’s premise. Customers do not have to queue for banking services but can do this at their own preferred time and place. The study aims at examining the effect of e-banking security on customer satisfaction in Uganda. To study the relationship between ebanking security and customer satisfaction, four security dimensions namely confidentiality, integrity, availability and authenticity are established based on literature review. The study uses a cross sectional survey methodology to gather data from 280 respondents. Results of correlation and regression analysis demonstrate that security has a positive relationship with customer satisfaction and therefore ebanking security has a big impact on predicting customer satisfaction. Various recommendations are put across on how retail banks can improve the security of their customer’s data hence satisfying them through the use of e-banking channels.