The question about the reality, nature and function of the Trinity in Christianity has evolved subjective theological and philosophical perspectives and debates among researchers, and more so is the issue of adapting the doctrine into African-initiated churches. The issue as it affects African Christianity in the Niger Delta has not been adequately addressed empirically. Thus, this study investigates and analyses the perceptions of Christians about the Trinity among selected African Initiated Churches. Quantitative research approach was adopted using a purposive sampling technique to explore the perceptions of selected church leaders about the concept of Trinity. Data were collected through the use of questionnaires from 50 selected church leaders from Celestial Church of Christ and the Apostolic Church in Niger Delta. The findings show that while most Christians understand the Trinity in terms of unity in diversity, some believe it is just mere normal church doctrine; whereas they all accept that there is timeless mystery of the Trinity beyond the mental construct of man from both churches. The study concluded that there is no consensus in the theological interpretation and conceptualisation of Trinity among African-initiated churches in the Niger Delta. Hence, the study recommends proper theological education as a means of addressing the problem wrong perception about the Trinity.