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This article seeks to highlight the challenges and issues that face merging higher education institutions and also to outline some of the challenges in integrating the quality assurance systems during the pre‐, interim and post‐merger phases in a merged university.

Case studies of merged and merging institutions were critiqued to compare the similarities and differences. A range of issues experienced by two universities that recently merged in South Africa is explored.

It is clear that merging institutions is a thorny issue, and cannot be resolved quickly. The merging of institutions brings with it a whole host of challenges. The current literature review has found that merging higher education institutions globally is invariably unpredictable, as the institutions experience multifaceted complexities.

The lessons learned from this newly merged university can be a very useful resource and guide to those in leadership positions.

This article contributes to the current pool of information and offers practical guidance and assistance to institutions that have merged or are in the process of merging.

Worldwide, higher education is undergoing major changes in its organisation. In this context, the concept of quality assurance control has emerged as a primary instrument for evaluating performance and accountability in higher education systems. South Africa is the latest candidate for a nationally imported system of quality assurance in the wake of several policy and legal initiatives to transform higher education after the demise of apartheid. Several contemporary developments, notably the South African Higher Education Bill and the Education White Paper 3 (Higher Education) are part of the government’s commitment to transform higher education. This paper will briefly discuss the origins and nature of quality assurance in South Africa. The article also critically reviews a number of conceptual frameworks about quality in higher education in order to develop a better and shared understanding of, and appropriate responses to quality assurance.