The purpose of this qualitative single-case study is to critically investigate the institutional, epistemological, and political friction experienced by dual-role academic–indigenous leaders at Makerere University as they navigate conflicting governance demands from traditional chiefly knowledge systems, corporate university management, and national political patronage networks. Guided by postcolonial institutionalism, the institutional logics perspective, and decolonial epistemic frameworks, the study examines how these leaders manage bureaucratic performance metrics, corporate auditing practices, and managerialist structures. Data collection involved 12 in-depth semi-structured interviews with eight dual-role academic–indigenous leaders and four senior public law practitioners, alongside a focus group discussion with six senior faculty members, for a total of 18 participants. This qualitative data was complemented by doctrinal analysis of key Ugandan public law decisions and statutes. Findings reveal a complex trialectic friction between communal, consensus-driven accountability rooted in ancestral custom; the hyper-individualised, metric-centric audit culture of New Public Management; and the dominant influence of national political patronage. Indigenous administrative lifeworlds and restorative practices are systematically marginalised or co-opted by rigid statutory compliance barriers and partisan networks. The study concludes that the uncritical adoption of New Public Management in African higher education breeds institutional alienation. It recommends statutory reforms by the National Council for Higher Education and the establishment of operationally insulated hybrid governance mechanisms within university councils to foster genuine epistemic pluralism.