The congregation organized in the late eighteenth century and originally built a smaller wooden church on the site.

An article dated August 19, 1853, said that a large window was directly behind the pulpit and was flanked by richly ornamented pilasters of the Corinthian order.

Methodists in Charleston purchased a half-acre lot at the southwest corner of Pitt and Calhoun streets in 1795 for use as a burial ground.

That year independent black congregations were prohibited by state law, following the Nat Turner's Rebellion of 1831 in Virginia.

With growth in the congregation, in 1852 they commissioned design and construction of a new building, the current Bethel Methodist Church, which was completed in 1853.

[3] During the 1886–87 period, an alcove was added behind the chancel for a pipe organ, carpet and pew cushions were put in, and stained glass windows were installed.

The unusual stenciling was applied to the interior walls in the late nineteenth century and is renewed each time the building is painted.