Background Stigma affects engagement with HIV healthcare services. We investigated the prevalence and experience of stigma among incarcerated people living with HIV (PLHIV) in selected South African correctional settings during roll-out of universal test and treat. Methods A cross-sectional mixed-methods study design included 219 incarcerated PLHIV and 30 in-depth interviews were conducted with four different types of PLHIV. HIV-related stigma was assessed through survey self-reporting and during the interviews. A descriptive analysis of HIV-related stigma was presented, supplemented with a thematic analysis of the interview transcripts. Results ART uptake was high (n = 198, 90.4%) and most reported HIV-related stigma (n = 192, 87.7%). The intersectional stigma occurring due to individual and structural stigma around provision of healthcare in these settings mostly contributed to perceived stigma through involuntary disclosure of HIV status. Interpersonal and intrapersonal factors led to negative coping behaviours. However, positive self-coping strategies and relationships with staff encouraged sustained engagement in care. Conclusion We encourage continuous peer support to reduce stigmatization of those infected with HIV and whose status may be disclosed inadvertently in the universal test and treat era.