This paper presents a case study of wellness programme and health policy development based on an HIV/AIDS organisation's Khayelitsha site in the Western Cape Province, South Africa. The study examines the different challenges that the organisation faces in relation to its predominantly low-income staff, donor-driven structure, its limited resources and organisational capacity, and the highly stressful and demanding nature of HIV-related treatment and care. This case study also examines the significant and contentious challenges lying in the organisation's faith-based identity. Research began with a review of civil society organisations' responses to HIV in sub-Saharan Africa, as well as related topics, such as South Africa's public health system, and health-seeking attitudes, beliefs and behaviours in high-risk South African communities. The organisation's health policy was analysed and 'workshopped' with multiple employees. Focus groups were conducted with mid-management and fieldwork staff in the Khayelitsha office, while a comprehensive, anonymous, wellness questionnaire was distributed in order to collect quantitative data. Data acquired from the questionnaire responses and the focus group discussions indicated that wellness programme and health policy development faces its greatest challenges on two fronts, namely due to a critical lack of organisational development and capacity, and a host of practical, social and cultural challenges among the most vulnerable people whom the NGO intends to serve. The study's primary recommendations include: taking its employees' cultural and social norms into consideration; addressing issues related to capacity and organisational development with the major donors; broadening the scope of its health policy to extend beyond issues related to HIV; and examining and clarifying expectations of employee behaviour in light of its identity as a faith-based organisation. The study also issues a secondary list of recommendations for other resource-constrained NGOs that also wish to develop and implement wellness programmes and health policies in their workplace.