Higher education reform is an international phenomenon and one that greatly impacts on the form and function of Universities in society. I set out in this study to investigate the University of Malawi’s (UNIMA) experiences with governance reforms after observing that no comprehensive study of this process had been undertaken following the implementation of these reforms from 1997. I used Bhaskar’s Critical Realist Theory as my main theoretical framework because my intention was to understand the mechanisms from which such reforms emerged: the emergent governance practices and properties enabling or constraining governance reforms in UNIMA. I employed Archer’s Social Realist Theory in my research design and interpretation of the results, which entailed that I focus on issues of structure, culture and agency in UNIMA governance. I have established that the governance context in UNIMA in 1995 at the time the reforms were being considered was one that promoted the continuation of the status quo because the Malawi Government’s vested interest then was to exercise great control over UNIMA at system, institutional and disciplinary level of governance due to the political imperatives of the time in Malawi. However, this situation was frustrating to many in the University as it greatly impeded academic freedom. Furthermore, in 1995 the University relied heavily on Government’s financial structures. When these were subjected to structural reforms under the influence of the World Bank and the International Monetary Fund in the early nineties the impact seriously undermined the University’s revenue base and threatened to challenge further the realization of the University’s objectives. This prompted changes in the administrative and academic governance structures and culture intended to improve utilisation of the available limited resources as well as to broaden the University’s revenue base. The governance reform measures that were introduced were mainly influenced by New Public Management (NPM) ideologies. Most of the reforms intended to transform the administrative structures and culture were successfully implemented. The study revealed that this was enabled by the interests of those operating at disciplinary levels who were frustrated by the previous constraining governance context and who viewed such reforms as bringing about the self-governance they lacked. However, the majority of the reforms that were mainly targeted at academic restructuring were resisted because they were construed as contradictory to the interests of those in the academy particularly those concerned with matters of academic freedom. The study further revealed that the academic reforms were constrained by a lack of agency for change management and weak leadership at the top senior level of the University. In addition, there have been delays in amending the UNIMA Act, which should have catalysed some of the reforms, a scenario that has perpetuated many aspects of the institutional level of governance. Consequently, compared to the situation before the reforms were introduced, governance in UNIMA at the time of reporting manifested two scenarios: (a) an elaboration in governance practices at systems level where Government machinery exercises control and at enterprise (college) level where faculties and academic departments operate promoting cultural morphogenesis, or changes at the level of ideas, beliefs and values, which in turn is exerting pressure on governance practices at institutional level; and (b) morphostasis, or lack of change, at institutional levels of the governance exacerbated by the lack of amendment of the UNIMA Act and weak leadership. The findings have also led to uncertainty regarding the unitary nature of the University. There are fears that once the UNIMA Act is amended the four colleges forming UNIMA might break away to become separate universities.