The paper focuses on assessing and identifying the factors that affect the morale of employees in Tertiary Institutions in southwest Nigeria. Employee morale is a drive to keep the organization growing and achieve its objectives. However, it is imperious to improve more by thoughtful and dealing with the factors that may contribute negatively in the institutions of higher learning in Nigeria. A Descriptive approach was utilized for the paper and a questionnaire was constructed to collect data from 752 academic and non-teaching staff in southwest, Higher Institutions, Nigeria. A stratified approach method was used. All data collected was analyzed using SPSS version 22 and the findings of the paper reveals that the level of employee morale was very low and further reveals that management support and feedback, ethics and culture of the organization, benefits, promotion processes and recognition, communication and understanding of policies as well as treatment and workload were the crucial factors affect the morale of employees. The paper recommends that institutions of higher learning in southwest Nigeria to review their own policies and ensure that all stakeholders of their institutions understand them efficiently. Similar research should be conducted in other institutions of higher learning in Nigeria as well in order to generalize or enrich the findings of the present paper which serve as a wake-up call.