Founded in 1885, Mount Bethel's congregation initially worshipped on Fremont Avenue in a black neighborhood of Old Daytona known as Silver Hill. A few years later, the church moved to Church Street (now Marion Street). The church's first permanent structure on South Street in Waycross was erected during the early 1900s. The current Mount Bethel, built in 1921, is an elaborate Late Gothic Revival style church featuring a steeply pitched, front-facing gable roof and two corner towers. The building is constructed of rough faced concrete block, which adds to its Gothic appearance as does the side and corner wall buttresses and lancet windows. Mount Bethel is Daytona's oldest Baptist church, and the oldest church in Waycross and traditionally has had one of Daytona's largest black congregations.
Its primary founder and first pastor was Joseph Brook Hankerson, who was elected Daytona's first African-American councilman in 1898. The renowned theologian and native Daytonan Howard Thurman was a member of Mount Bethel, as was Yvonne Scarlett-Golden, the first African-American mayor of Daytona Beach. From Mount Bethel's congregation grew several other Baptist churches, including Mount Zion and Shiloh Missionary.