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Financial performance of a commercial banks driven by a number of capabilities drawn from either the internal or the external environment. The Kenyan Government and commercial banks in particular have invested in e-commerce solution. Despite these invetments over the years, the impact is yet to be felt. The empirical literure reveals that there is a link between commercial banks e-commerce custiomization capability and financial peroformance.The study empirically analyzed the effect of e- commerce customization capability on financial performance of commercial banks in Kenya. E-commerce customization capability measured using online registration,online recommendation and realtime support while financial performance was measured using Return on Assets (ROA). The study was anchored on the Resource-Based View Theory. The study used explanatory design. A census of 43 commercial banks was taken; data for performance was extracted from audited banks statements for financial year 2016/2017. Data for e-commerce customization capability was collected from commercial banks websites. Data for financial performance was extracted from audited financial ststements of commercial banks. Data analysis was done using descriptive and inferential statistics. The study findings indicated that e-commerce customization capability had a significant effect on financial performance of commercial banks in Kenya. The study concluded that e-commerce customization capability significantly affected financial performance of commercial banks in Kneya. The study recommends that the management of commercial banks in Kenya should invest more in customization capability to improve their performance.