Universities in South Africa seem to be struggling to create inclusive conditions for black students to succeed in their studies. The persistence of inequality in universities could be partly blamed on the use of the term 'historically disadvantaged', which is not defined in policy documents, and this has resulted in universities being unclear on what exactly to address in their transformation. Using the capability approach in this study, it is argued that policy should address the structural, institutional and environmental factors that contribute to student disadvantage, which prevent the development of opportunities and agency among students. Seven semi-structured interviews were conducted to collect qualitative data from key stakeholders who dealt with student affairs (university staff and student representative council [SRC] members) at one South African university with the aim of developing an understanding of student disadvantage from their perspective. The findings revealed that student disadvantage manifests through structural and institutional factors, namely a culture of racism, alienating university campuses, student poverty, university teaching, and gender inequality. The study recommends that universities consider addressing these factors in their transformation.