Higher educational institutions continuously look for ways to improve the quality of its eLearning capacity and adapt learning solutions suitable to the needs of the institution. During the 2016 Fall Semester, Southern University and A & M decided to transition from the Blackboard learning management system (LMS) to the Moodle learning management system (LMS). Typically such transition present a huge challenge for the University, Faculty and Students. Additionally, on August 2016, what CNN themed “the worst natural disaster, to strike the United States since Hurricane Sandy” [1], occurred in Louisiana during the transition. This led to massive disruptions in academic and economic activities in the state. This paper examines the perceptions of both faculty and student on the transition from one LMS to another and also what impact if any the natural disaster had on the process. Faculty and students were surveyed to gain understanding of how they perceive the transitioning process and their perception of both LMS, their preferences and why. Furthermore, we identified issues peculiar to transitioning during a natural disaster. The results of this study can be used to anticipate issues that may be associated with transitioning from one LMS to the other and issues peculiar to transitioning amidst a natural disaster. It can also be used to identify areas for improvement.