Background Despite aspects of the SAFE strategy for reducing trachoma in Tanzania have been somewhat successful, the disease still persists in marginalised communities even with repeated trachoma control interventions. This study aims to understand the facilitators and barriers associated with implementing trachoma control programmes in these communities, from the perspective of non-governmental organisations (NGOs). Methods Participants were the representatives of NGOs who had knowledge and experience in the implementation of trachoma control programmes. Data was collected using in-depth, semi-structured interviews guided by a topic guide, which was updated after each interview using a constant comparative method. Interviews were audio-recorded and then transcribed verbatim. Thematic analysis was done inductively. Codes were generated from the transcripts and then clustered into themes. Findings The context within marginalised communities often acted as a perceived barrier to successful implementation of control programmes. This included poor environmental cleanliness, lack of trust, poor disease knowledge and traditional lifestyles. Community values could either be a facilitator or a barrier, depending on the scenario. The anatomical location of the disease and the poor understanding of the disease progression also served as barriers. Considerations affecting decision-making among NGO’s include financial feasibility, community needs and whether the quality of the intervention could be improved. NGOs felt that the collaboration and the opportunity to learn from other organisations were beneficial aspects of having different actors. However, this also resulted in variability in the effectiveness of interventions between districts. Conclusion NGOs should focus on behaviour change and health education that is tailored to marginalised communities and seek innovative ways to implement trachoma intervention programmes whilst being minimally intrusive to the traditional way of life. Partners should also implement ways to ensure high quality programmes are being provided, by increasing staff accountability and compensating volunteers fairly.