The history of Port Gibson Baptist Church has been traced to the Magnolia Baptist Church about four miles southwest of Port Gibson, where Baptist of Claiborne County worshipped in the early days of the county. According to Rev. D. I. Purser, missionary to Union Association, ". . . The old Magnolia Church was found numbering twelve members and the house was without seats. The house was much injured by shot and shell during the Civil War since it was in the midst of a battlefield. Soon after, Port Gibson was visited . . . where there had never been an organized Baptist church. . . . With much difficulty a house was obtained where worship services were held until the second Sabbath of May. Then, assisted by Brother James Nelson, a meeting was held . . . which resulted in the organization of a church with nine members." Records show that on May 22, 1872, nine members of the Magnolia Baptist Church were granted letters of dismission "to go into constitution of a church in Port Gibson." Rev. Purser served as first pastor and the church was known as "First Baptist Church of Port Gibson." His annual salary was $1000.

The congregation first met in the Presbyterian Church, and later in a schoolhouse in the town. On June 3, 1873, the Baptists purchased a lot on College Street for $200 on which their first building was erected. Years of hardship followed in which a boll weevil plague, yellow fever, and loss of membership led to financial difficulty and, finally, the loss of the building due to the inability to meet payments. But the Port Gibson Baptist persevered in their desire to fulfill the Great Commission. In 1895 a new building was erected at the corner of College and Jackson Streets, where they worshipped until 1923. The present building at Carroll and Church Streets was completed and dedicated in 1923. Next door to the church was the pastor's home. Rev. S. P. Morris was pastor.