Understanding the role of contextual factors beyond individual behavioural determinants is critical to identify strategies to achieve engagement in HIV clinical care. We sought to examine how subjective and objective evaluations of clinic-level costs and value placed on allopathic care influenced HIV care engagement. We used repeat in-depth interviews over 6 months among newly HIV diagnosed adults in South Africa. Data were analysed using thematic analyses and framework matrices to explore individual trajectories over time. Three main patterns of care engagement emerged: failure to enrol in care within 3 months, disengagement after enrolment, and early enrolment with sustained engagement. Findings show that burdensome health systems coupled with low perceptions of the future value of HIV care, compromise HIV care engagement. Without addressing these costs and enhancing perceptions of value on clinical care, the number of people engaging in HIV care is likely to fall short of goals.