Grounded in the qualitative tradition, the aim of this study was to explore how principals perceive the processes governing, tensions inherent in and consequences, of the secularisation of public schools in South Africa, against the backdrop of the old apartheid system. Principals are key informants who bridge the gap between the political arena and the individuals who are affected at the implementation level and therefore provide a valuable lens through which the process of secularisation can be explored. Eight principals, who had been in this position of leadership for at least eight years, participated in semi-structured interviews, which were then subjected to a thematic content analysis. Principals perceived the process as characterised by a lack of consultation and transparency, with no clear guidelines provided to them and no follow-through from the education ministry. They also perceived tensions in the manner in which principals continued to embrace Christian principles in the management of their schools. Tolerance and respect of different religions were identified as positive outcomes of secularisation but these were perceived to have been offset by the negative consequences of a moral collapse, an ungovernable school and a loss of identity among the students. Through exploring the nature of key socialising agents, in the educational arena, it became evident that the participants often conceptualised themselves as martyrs and perceived parents as morally neglectful. The changing role of the school, as an agent of religious education, was also explored. Overall, all the principals strongly agreed that despite the good intentions of the government in fostering a democratic society, the impact of secularisation had resulted in some unintended effects, including a negative impact on the moral development of the students. In sum they perceived that the negative consequences of secularisation outweighed the promises of the government’s overall secularisation vision.