The Zion A. M. E. Church of Williamsburgh was organized in 1832 by Thomas Watson, in his house on Third (Berry) Street between North 4th and North 5th Streets. The church later rented rooms on North 4th Street between Third and Fourth Street (Berry and Bedford). The congregation numbered 12 members at this time, and retained Rev. John Churchill as its first regular preacher. Churchill also taught at the African Free School (later Colored School No. 3).
Organized on 18 June 1842 and Incorporated in 1844. William Harden, a blind Black preacher was the first and only leader of the church. The first place of worship was in a rope walk, and after that burned the congregation met in private houses. After Harden's death in 1847, the congregation split up, with most of the worshippers moving over to the African M. E. Church on High Street.
This congregation was a spin-off from Sands Street M. E. Church. On 18 January 1818 the church was incorporated as a satellite of the Sands Street M. E. Church, after the number of Black congregants at that church exceeded the capacity of the "colored gallery" there. In 1819, the trustees of Sands Street imposed a fee of $10 per quarter on the Black worshippers, compelling the majority of them to secede to form their own church. The first trustees for the congregation were Peter Cruger, Israel Jemison, Caesar Sprong, Benjamin Cruger and John E. Jackson.