The first Methodist Church in Waynesboro was formed sometime between 1812 and 1815. A church building was erected at what is now the northwest corner of Jones Avenue and Seventh Street. This house of worship served the Methodists prior to the Civil War. The first mention of the church is found in the Ogeechee District of the South Carolina Conference in 1823. It moved to the Savannah District of the South Carolina Conference in 1825 and, finally, to the Georgia Conference in 1831. It joined the South Georgia Conference in 1866 when the conference was created. In 1880, this lot was conveyed by the Board of Trustees of the Waynesboro Methodist Church to Mr. Simeon A. Gray. In the conveyance of describing the property, the following language was used, "being the old Methodist Church lot occupied and held for a long period of time by the above-named church."
On September 21, 1857, a lot was purchased from Mr. Edward J. Carter, bound by Liberty Street, Joel Street, and Myrick Street which is the present location of the church building. On the lot at least four church buildings have been built by this congregation. The conveyance in 1857 was made by John J. Jones as a trustee for the church. A church building was quickly erected on this site and was remodeled in 1880. In 1896, the building had become too small and the trustees moved the wooden building to a point on Liberty Street and Eleventh Street, donating the building to an African American congregation. This wooden building was later moved to Quaker Road and Eleventh Street where it remains today.
A new frame building was erected in 1896 but was destroyed by fire in 1907. A brick building was built in 1907 but was also destroyed by fire on December 19, 1936. The west wall and towers, however, were able to be used for a new brick building completed in 1938 and standing today. This present structure was completed under the direction of Mr. Arthur J. Evans, Chairman of the Board of Stewards, and Rev. Lawrence Gray, pastor.
An Education building with a Chapel and Fellowship Hall were completed in the late 1960s. During the 1990s, additional property was deeded to the church for parking lot space. The Dinwiddie House was a part of this addition and was remodeled as office space. In 2017, the church completed phase one of a multipurpose building to aid in the growing children's and youth ministries. The church sanctuary seats approximately four hundred persons and is adorned with smaller stained-glass windows and by three large, stained-glass windows; one of the Nativity, one of the Announcement to the Shepherds, and one of the Resurrection.