HIV stigma and discrimination are a major challenge facing people living with HIV (PLHIV) globally. As part of a larger qualitative study with PLHIV in Yogyakarta and Belu, Indonesia, this paper describes the participants’ perceptions about drivers of HIV stigma and discrimination towards them within families, communities and healthcare settings, and highlights issues of HIV stigma as a social process. Participants were recruited using a snowball sampling technique. Data analysis was guided by the framework analysis for qualitative data, and conceptualization and discussion of the study findings were guided by the HIV stigma framework. The findings showed that participants experienced stigma and discrimination across settings, including in families and communities by family and community members, and in healthcare settings by healthcare professionals. The lack of knowledge about HIV, fear of contracting HIV, social and moral perceptions about HIV and PLHIV were perceived facilitators or drivers of stigma and discrimination towards PLHIV. HIV stigma and discrimination were also identified as a process linked to the whole groups of people within families or communities, which occurred within social context in Yogyakarta and Belu. The findings indicate the need for HIV education for family and community members, and healthcare providers to enhance their knowledge of HIV and improve acceptance of PLHIV within families, communities and healthcare settings.