Objectives Stigma remains pervasive for people living with HIV (PLHIV) in sub-Saharan Africa, undermining care engagement. Using everyday, biographical and epochal temporalities, we explored the manifestation of stigma at different stages of the HIV care continuum in seven health and demographic surveillance sites in Eastern and Southern Africa. Methods Between 2015 and 2016, we conducted qualitative in-depth interviews with 264 PLHIV, 54 health providers and 48 family members of people who had died from HIV. Topic guides explored experiences of HIV testing, care and treatment services. Data were analysed thematically, aided by NVivo 10. Results In everyday time across these communities, stigma was evident in the presence of gossiping and the relative absence of supportive interpersonal discourse, which fuelled judicious disclosure. This was especially disruptive at testing, counselling and early antiretroviral therapy adherence stages of care. Biographical time framed everyday stigma events, highlighting the dilemma of disclosure in relation to sexual relationship norms, as well as the interfacing of age and healthcare continuum points. Epochal patriarchal relations gave a structural context to everyday and biographical stigma dynamics. Historical shifts to social acceptance of PLHIV within these communities, while positive, were complicated by stigma in everyday life and in respect of biographical goals like having a family. Moreover, low community-level resistance to HIV-related stigma jeopardised stigma reduction strategies. Conclusions Despite improvements to HIV care services, stigma remains pervasive across the HIV care continuum in these sites. Context-specific interventions are needed to address stigma and discrimination of PLHIV within the community and in health services, and greater reflection is required to ensure policies aiming to expand HIV treatment do not exacerbate stigma and result in negative HIV outcomes