Purpose In spite of the effectiveness of opioid antagonist treatment (OAT) in reducing injecting drug use and needle sharing, programmes in prison continue to be largely stigmatised. This affects programme participation and the quality of programmes delivered. This study aims to explore how Indonesian prison staff and prisoners perceived and experienced stigma relating to prison OAT programmes and identify potential strategies to alleviate this stigma. Design/methodology/approach Three prisons in Indonesia were selected as part of a qualitative case study. Two of the prisons provided OAT, in the form of methadone maintenance treatment (MMT). Purposive and snowball sampling were used to recruit study participants. In total, 57 semi-structured interviews were conducted with prison governors, health-care staff, prison officers and prisoners. Prisoners included both participants and non-participants in methadone programmes. The data were analysed thematically. Findings MMT programme participants were perceived by both prison staff and other prisoners to be engaged in illicit drug use, and as lazy, poor, dirty and unproductive people. They were also presumed to be HIV-positive. These multi-layered, intersectional sources of (inter-personal) stigma amplified the effects on prisoners affecting not only their quality of life and mental health but also their access to prison parole programmes, and therefore the possibility of early release. In addition, organisational factors – notably non-confidential programme delivery and lack of both family and institutional supports for methadone prisoners – exacerbated the stigmatisation of MMT programme participants. Practical implications Effective strategies to alleviate stigma surrounding OAT programmes such as MMT programmes are urgently needed to ensure participation in and the quality of programmes in prisons. Originality/value Many prisoners reported experiencing stigma relating to their participation in MMT programmes in both the methadone prisons studied. They often emphasised the ways that this stigmatisation was amplified by the ways that MMT programme participation was associated with drug use and HIV infection. However, these intersecting experiences and concerns were not recognised by health-care staff or other prison staff. Effective strategies to alleviate stigma surrounding OAT programmes such as MMT programmes are urgently needed to ensure participation in and the quality of programmes in prisons.