Information system (IS) acceptance has been the subject of much research in the past two decades. Researchers have concentrated their efforts on identifying the conditions or factors that could facilitate the acceptance of information system (IS) into microfinance banks. The purpose of this paper is to find out if there is a significant relationship between security and acceptance of web based marketing information system (MKIs) among micro- finance banks in Nairobi Region, Kenya. It also tends to provide deeper understanding on the current security and acceptance level of web based MKIS. Anonymous and self-administered questionnaires were distributed to 383 respondents. A total of 370 usable responses were received, resulting in a response rate of 96.6% which was considered satisfactory for subsequent analysis. Due to the quantitative nature of the study, the results are analysed with statistical measures. The results indicated that Security was influential determinant of acceptance with t= 2.0541, β= 0.120, p< 0.01 at 1% significant level though most respondents indicated that the current security level of the system was low. Theoretical contributions and practical implications of the findings are discussed and suggestions for future research are presented.