This brick Gothic Revival-style church with its tall steeple replaced an earlier 1872 church badly damaged by the 1886 earthquake. Built in 1891, it retains its original alter, communion rail, pews, and light fixtures. The sanctuary is one of only a few unaltered religious interiors in Charleston that date from the Victorian period. Today Emanuel is the oldest AME church in the South and houses the oldest black congregation south of Baltimore, MD.

The history of this congregation reflects the development of religious institutions for African Americans in Charleston. Its roots stem from a religious group of free blacks and slaves organized in 1791. In 1816, black members of Charleston's Methodist Episcopal Church withdrew over disputed burial ground, and under the leadership of Morris Brown, formed a separate congregation. The church's 1,400 members soon after established themselves an African Methodist Episcopal church, a denomination formally established in that same year in Philadelphia, Pa. Two years later, Brown and other ministers of the church were jailed for violating state and local laws which prohibited religious gatherings of slaves and free blacks independent of white supervision.