The purpose of this study was to examine challenges facing the Church in dealing with Moral Issues and the way forward in Ghana. Qualitatively, the study sought to examine the Church's challenges in coping with Moral Issues and the way forward in Ghana. The study adopted a case study research design. The population of the study comprised leaders of Calvary Baptist Church – Adabraka and Shiashe. These include the Vice President of the Ghana Baptist Convention and departmental heads at the Ghana Baptist Convention headquarters. Others included the Senior Pastor of Calvary Baptist Church – Adabraka with its satellite mission at Shiashe as well as a cross-section of pastors of these churches; the church administrator; the past and present directors of Baptist Relief and Development Agency (BREDA). The purposive sampling technique was specifically used to locate respondents for the study. The churches and participants were chosen because of their efforts in dealing with the causes of immorality confronting Ghanaian society. The main tool for data collection was a semi-structured interview guide. The data gathered was organised and analysed manually using emerging themes. The study revealed that the challenges which the Baptist Church encounters in its effort to deal with moral issues are the politicisation of statements made by the clergy, and inadequate trained personnel who are willing and ready to champion the agenda of the church in that respect. Financial difficulties were also mentioned. In this regard, specific reference was made to the effort made by the Ghana Baptist Convention to free the Trokosi girls. It was indicated that it takes a lot of financial resources to train and settle the freed girls. Regarding the way forward as far as these challenges were concerned, it was suggested that the church ought to speak more and do what it is mandated by Christ to do to bring about transformation. It is recommended that Churches should seriously intensify education on what constitutes human rights and freedom so that there would be a clear understanding of the concept that enables people to think through and adopt the good aspects to enhance their circumstances. Human rights defenders should exercise restraints when it comes to practices which are alien to Ghanaian values, laws and religious faith.