Worldwide, it is acknowledged that education is the engine of national development as it empowers individuals to improve their skills and reduce inequality on various fronts. Higher education plays a significant role as agents in achieving Sustainable Development Goals (SDGs). The drive for quality assurance in higher educational institutions has recently become key, especially when evaluating their performance. The establishment of quality assurance offices and setting regional, national and university policy frameworks are some of the key strategies to improve quality of education. Despite the quality assurance institutionalization and the policy frameworks in place, the general performance of universities remains problematic. Using documentary review of literature, focus group discussions and interviews of academic staff in two East Africa Universities, this paper documents and examines the difficulties in implementing quality assurance systems in African Public Universities. The study discovered that scarce financial resources, inadequate human resources, negative perceptions, lack of better understanding about what the Office of Quality Assurance does and doesn’t do and poor physical infrastructure are the major difficulties hindering the implementation of effective quality assurance systems in higher institutions of learning. Ideas for improvement include availing more funds to the quality assurance units and granting them more autonomy.