In Muslim societies, practitioners often find that standard ethical codes and LGBT-inclusive guidelines stand in direct opposition to their religious doctrines. This divergence between professional mandates and personal faith inevitably triggers significant value conflicts for Muslim counsellors. The purpose of this grounded theory study is to develop a theory that explains how Muslim counsellors experience value conflicts in counselling Muslim LGBT clients and how they resolve the conflicts. In-depth interviews were conducted with six Muslim counsellors at Public Institutions of Higher Education (PIHE) in Peninsular Malaysia using the grounded theory approach of Theoretical Sampling. The grounded theory process of data analysis was employed, starting with open coding, axial coding, and selective coding (Strauss & Corbin, 1990, 2008). The findings revealed that the Muslim counsellors wanted to achieve two therapeutic goals in counselling Muslim LGBT clients: giving insights and bringing about positive changes. To achieve those two goals, they go through four processes namely, building rapport, integrating religious values, facing conflicts and challenges and overcoming them.