InIn 1894, members of Sandy Run Methodist Church organized this church in Bonaire community, south of their community. The land was donated by William S. King
. Rev. J. R. Owen was the first pastor. As the church grew, Sunday school rooms and restrooms were added to the rear of the wooden sanctuary in the mid-1950s. Later the brick fellowship hall and classrooms were built next to the sanctuary. Land for a community cemetery, currently supervised by the Bonaire Community Cemetery Corporation, was also donated by Mr. King. In 1919, this church was part of the Elko Circuit of the Cordele District. In 1940, it was still in the Elko Circuit, now part of the Macon District.
In 1959, the Week Day Kindergarten was organized. During the 1960s the interior of the sanctuary was renovated, adding a balcony, replacing pews, and changing from two aisles to one. Cub Scout and Girl Scout troops were started. During the 1980s the parsonage was purchased, a front porch and steeple were added to the church, and vinyl siding installed. Stained glass windows were added in 1990. The church celebrated its Centennial in 1994. In 1997-1998 the church purchased its present sanctuary building from the Bonaire Baptist Church. The first service was Easter Sunday. The church still owns the older sanctuary building.