The roots of the African Methodist Episcopal Zion Church lie in the same discrimination that produced the AME Church, though the two arose independently in different cities. In New York, Black members of the John Street Methodist Episcopal Church, including the class leader James Varick, grew weary of segregated seating and a refusal to ordain Black preachers, and in 1796 they began worshipping separately, initially still under white Methodist supervision. They built their own building, Zion Chapel, on Church Street in 1800, the origin of the denomination's name. For two more decades the congregation pressed for full independence, and on September 13, 1820, Varick and Abraham Thompson were ordained elders in a decisive break from white oversight; the following year, delegates meeting in New York formally organized the African Methodist Episcopal Zion Church and elected Varick its first superintendent, a title soon changed to bishop.
The new denomination quickly became known as the Freedom Church for its deep entanglement with abolitionism. Frederick Douglass preached from its pulpits and was for a time a licensed local preacher in the connexion; Harriet Tubman worshipped and organized within it; and Sojourner Truth was among its members. Zion congregations served as stations on the Underground Railroad, and the denomination was, from its earliest years, a base for Black political organizing as much as a church.