Electronic commerce plays a major role in any society’s socio-economic progress, and now forms a fundamental part of the way people and organizations purchase products, services and conduct business. Still, its full potential still remains unfulfilled. The realisation of its potential in in Kenya will only be achieved once existing challenges, such as lack of trust and security, are eliminated. This paper had two objectives: to assess the factors that affect users’ level of trust and sense of security in E-Commerce applications; To establish the relationship between trust and security in E-Commerce applications. The researcher applied mixed methods research; and data collection was done by using a questionnaire, followed by focus group discussion. The results point to the existence of an intricate relationship between user’s level of trust and sense of security. Further, it was deduced that lack of security affects trust levels which leads to reduced online transactions. There is need for e-commerce organizations to ensure that adequate security measures are employed in order to gain a larger market and to increase profitability.