OBJECTIVES: HIV prevalence and incidence are higher among key populations including Men who have Sex with Men (MSM) and transgender women in low and middle income countries, when compared to the general population. Despite World Health Organisation guidelines on the provision of services to key populations recommending an evidence-based, culturally relevant and rights-based approach, uptake of HIV services in many resource-limited and rights-constrained settings remains low. Médecins Sans Frontières (MSF) has been offering health services for MSM and transgender women in Beira, Mozambique since 2014 using a peer-educator driven model, but uptake of services has not been as high as expected. This qualitative study aimed to learn more about these key populations in Beira, their experiences of accessing MSM- and transgender-friendly services and their use of face-to-face and virtual networks, including social media, for engagement with health care. METHODS: In-depth interviews were carried out with MSM and transgender women who were 1) enrolled in, 2) disengaged from or 3) never engaged in MSF's programme. Purposive and snowball sampling were used to recruit the different groups of interviewees. Interviews were conducted in Portuguese, transcribed and translated into English before being coded and manually analysed using a thematic network framework. RESULTS: Nine transgender women and 18 cisgender MSM participated in the study. Interviewees ranged in age from 19 to 47 years, with a median age of 29. Three main themes emerged from the data: perceptions of stigma and discrimination, experiences of the peer-educator driven model and the use of face-to-face and virtual platforms for communication and engagement, including social media. Interviewees reported experiencing stigma and discrimination because of their gender or sexual identity. HIV-related stigma and health-care setting discrimination, including gossip and breach of confidentiality, were also reported. Although the presence of the peer-educators and their outreach activities were appreciated, they had limited visibility and an over-focus on health and HIV. The face-to-face networks of MSM and transgender women were small and fragmented. Virtual networks such as Facebook were mainly used for flirting, dating and informal communication. Most interviewees were at ease using social media and would consider it as a means of engaging with health messaging. CONCLUSIONS: MSM and transgender women have challenges in accessing health services due to being stigmatised because of their gender identity and their sexual behaviour, and often experience stigma at home, in health-care facilities and in their communities. Peer-driven models of engagement were appreciated but have limitations. There is an untapped potential for further expansion and engagement with face-to-face and virtual platforms to reach MSM and transgender women in settings with a high HIV burden, and to provide them with essential information about HIV and their health.