Freedmen established this historic congregation in 1867. James McGill writes in his fascinating book, The First One Hundred Years of Upson County Negro History (2017): By the summer of 1870, Reverend William Harris was sent to St. Mary AME Church in Thomaston, Georgia. Rev. Harris, the third pastor in the history of St. Mary, was born free in Hartford, Connecticut, in 1845 but was kidnapped in 1858 and sold into slavery in Georgia. He escaped to the North two years later and eventually enlisted in the Union Army.
William Harris met Rev. M. Turner, a Presiding Elder of the AME Church, on the corner of Peachtree and Whitehall Streets in Atlanta in 1866…At the Atlanta Georgia District Conference of the AME Church, Rev. Turner licensed [Harris] as an exhorter, and then presented him a preacher’s license at the Wilmington Annual Conference in Wilmington, North Carolina. Rev. Harris received some schooling at what would later become Clarke College. Rev. Harris served Atlanta’s Western Mission for two years before being presented a deacon’s license in 1870 and appointed to St. Mary in Thomaston.
It is safe to assume that Rev. Harris taught school at St. Mary AME Church. St. Mary had a new church building completed that year  which provided ample room for scholars. The school operated in St. Mary at least as late as 1876. Upson County did not open a public school in Thomaston for Negro students until August 1883; St. Mary can confidently claim credit for housing the first successful church school organized for the Negroes in Upson County.
The current church building was constructed in 1905 during the pastorate of Rev. J. H. Adams. Trustees were: H. R. Rogers; Ed Hix; A. G. Cary; George Bell; William Brown; James Brown; James W. Bell; M. Drake, Sr.; and A. Holsey. The church retains its original appearance, though stucco has been applied to the original brick.