The Chaplaincy is headed spiritually by the Chancellor of the University. The Chaplaincy Board constituted by the Chancellor is the decision-making body on spiritual matters. All the spiritual development programmes and administration are handled by the Chaplaincy as coordinated by the University Chaplain. The Chaplain is supported by the Chaplaincy team which includes: Deputy Chaplain, Associate Chaplain, Pastors drawn from the Living Faith Church who is either members of faculty or staff of the University, who also are assigned various responsibilities from time to time and other administrative staff. The Student Chaplaincy body includes the student Chaplains and Chapel Unit Executives.

The Chaplaincy mission is to generate spiritual programmes designed to achieve the Vision and Mission of Covenant University. The spiritual life of students is enhanced through pastoral care services, counselling, spiritual development, chapel programmes, workshops and conventions, Bible studies, community outreaches etc.

The Chapel is intended to bring the faculty, staff, students and other members of the university community together for worship, spiritual nurture and moral education. Covenant University is a Christian Mission University; hence our approach to spiritual development is based on principles and practices drawn from the Holy Bible. The Bible remains our standard source of reference in all issues of life, be it academic, social or spiritual.