Bethany Baptist was formed on September 8, 1828, with six founding members—three men and three women. Harris County itself had been established only the year before, in 1827, following the Second Treaty of Indian Springs, which ceded the last Creek lands between the Flint River and the Chattahoochee. Bethany was therefore among the very first churches organized in the new territory.

A detailed church history compiled by Lillian D. Champion in History of Bethany Baptist Church, Pine Mountain, Georgia 1828–1978 traces the congregation's early years. The first church was built in 1830 at Goodman's Crossroads, about a quarter mile southeast of the present site. A second sanctuary was constructed in 1838, approximately two miles north of the current location. In 1847, Joel Culpepper deeded 7½ acres for "religious purposes and a burying ground," and that same year, the present church was erected.

Though the building has undergone many improvements, the original 1847 framework remains intact. Membership grew quickly—73 by 1836, 147 by 1845, and 152 by 1861, just as the Civil War began. Of those 152 members, 106 were white and 46 were Black, reflecting the complex realities of the era.

Bethany Baptist has endured through wars, social change, and shifting populations, continuing to serve its community after nearly 200 years. The cemetery is a vital part of its story. According to Find a Grave, there are 438 documented burials, 69 dating before 1900. Each grave tells another piece of the long and layered history of this congregation. From its beginnings as a small gathering of six members to a church that has stood for generations, Bethany Baptist remains a testament to perseverance, faith, and community in rural Georgia.