Traditionally, a chaplain is a cleric such as a priest or imam of a religious tradition, who provides spiritual support, and care to secular institution, workplace or private chapel. Faith based universities are institutions of higher learning that integrate religious beliefs and values into their campus life. Globally, institutions of higher learning experience several activities every day and some bring severe challenges to the development of the institutions and the personalities involved. Scholars in various academic fields have carried out research on these activities, which include the decline of morality, drug abuse, examination malpractices, gangsterism culture, cultism, obscene dressing and sexual promiscuity, harassment, unruly behaviours to lecturers and other constituted authority. However, adequate attention has not been paid to the influence of religious programmes and activities of the chaplaincy in the tertiary institutions. This is the onus of this paper in attempting to fill the gap in literature by exploring the influence of Chaplaincy activities on Moral and spiritual transformations of selected Faith based Universities in Southwest Nigeria as well as evaluate the impact of chaplaincy activities on the ethos of the university community. Through the administration of questionnaire, interviews and review of literatures, hinged on the application of structural theory of functionalism, this paper argues that there are inbuilt personality traits seen in students who experience psychological and behavioural challenges. These traits impeded their learning and moral development. The findings further revealed religious activities in the campuses through the activities of the Chaplain have moderated the major moral challenges facing students therefore, the chaplaincy pastoral, care and counselling should be applied in intervening and remedying these obnoxious challenges .This paper recommends that all faith-based institutions of higher learning in the south west of Nigeria should improve the services of chaplains and develop new paradigms for effective whole-person development of students in their institutions through chaplaincy ministry in the institutions of higher learning