In the last few years, most Kenyan universities have adopted E-Learning as a new approach to teaching and learning. However, the explosive growth and usage of mobile applications and the emergence of mobile cloud computing concept has brought about unresolved challenges related to the security regarding the reliability and privacy of devices in E-Learning. These challenges faced by universities have continued to impact negatively on the effective utilization of mobile cloud in E-Learning. This research thus sought to investigate current challenges that affect the security of mobile cloud environment to E-Learning users, their network platform and data stored on the mobile devices with regard to issues of privacy, data ownership and concerns about device access and security. Focusing on cloud computing Software As a Service (SAAS), most users store huge and sensitive data downloaded from the cloud. The researcher therefore sought to analyze the security challenges brought about by mobile cloud and discover the existing current security standards, models, frameworks and their shortcomings in addressing comprehensive security whilst using the available major security goals and attributes as a weighing factor. This descriptive research utilized a cross-sectional survey research design that involved quantitative techniques. Purposive sampling was used to determine the number of participants while close-ended questionnaires was used as a tool to collect the data from respondents who included the students registered in E-Learning, lecturers, Staff and senior administrators involved. Face validity and content validity was carried out through expert opinions. Descriptive statistics and inferential statistics were used for the data analysis to achieve results. The resultant framework established a secure and comprehensive environment for mobile cloud computing by borrowing from other developed frameworks that assisted in the mapping out of security risks and controls that current and prospective users need to take care of to ensure its secure implementation in higher education institutions and in Kenya as a whole.