This article explored challenges experienced in merged higher education institutions during restructuring using a selected comprehensive university (CU). As part of its restructuring, the CU abandoned the unitary governance model it had adopted when it merged and opted for a new governance model — the divisional governance and management (DGM) model. This was to consolidate the problematic merger and expedite the achievement of the objectives of the National Plan for Higher Education (NPHE). The governance model being investigated here is important because it is unique in the South African higher education context (Stumpf, 2008). It has been adopted in only one merged South African university, the North West University; it has not been attempted anywhere else in the merged South African universities (Mantashe, 2013). Semi-structured interviews were conducted with 39 respondents, purposively selected for data collection. The findings revealed the following challenges: resistance to change, lack of clear reporting lines, inadequate financial resources and high costs of implementing the new governance model, unequal treatment of the different campuses or sites of the merged university, inconsistent application of institutional policies across the different campuses of the merged institution, the institutional culture, highly unionised institution, leadership instability, and inadequate communication. Based on the findings of the research, the study provided some recommendations to address the challenges identified by the study.