One of Athens' youngest Presbyterian Churches, Covenant was officially established in May 1966, with 33 members. The congregation met in the Gaines Community Center until 1970, at which time it moved to the Presbyterian Center on the campus of the University of Georgia. With the assistance of other Presbyterian churches in Athens, long-range plans came into focus. On May 2, 1971, Covenant Church moved into its multi-purpose building on Gaines School Road. Since the early days of organization, the membership has grown to over 400 confirmed members.

In November of 1975, the Christian Education Building was completed. The following summer some of Covenant's own members finished the basement into one large and two smaller rooms. In March of 1986, the Worship Center was completed. In 1995, the remainder of the facility was completed with space for offices, music and choir, library, and four additional classrooms, and the original Fellowship Hall renovated.

The program of the church includes many aspects of worship, study, outreach, and fellowship. In collaboration with the Witness Ministry team and the Northeast Georgia Presbytery, the congregation is involved in responding to the spiritual and social needs of this rapidly growing segment of Athens. Covenant also shares the facility with many groups and organizations in the Athens community, such as Alcoholics Anonymous, Cub Scouts, Square Dancers, and residential community associations. Covenant supports ministry to students through the Presbyterian Student Center at the University of Georgia. Covenant Church is a member of the Northeast Georgia Presbytery, Synod of the South Atlantic, and the General Assembly of the Presbyterian Church (USA). The congregation reflects the rich diversity of the Athens community and all members are given an opportunity to share their gifts in Christian ministry.