The AFM was a self-propagating movement early on due to the successful evangelism of Boer and African converts. In 1909, Lake wrote to The Upper Room, an American Pentecostal journal, that missionaries were not needed as the AFM had men “far superior to any that can come from America who can speak English, Dutch, Zulu, and Basuto”. Towns and mining compounds were prime areas for missionary activity, reflected by the fact that 69 percent of AFM members lived in urban areas in 1928. From urban centers, the AFM spread to rural areas through returning labor migrants or native preachers.

The interracial character of the AFM was, like American Pentecostalism, short-lived. One explanation for this shift was tensions over economic competition between poorer whites and blacks. In July 1909, it was decided that baptisms of whites, blacks, and coloureds would be separate. Lake even addressed the South African Parliament, which he advised to adopt a policy of racial segregation similar to the policy for Native Americans in the United States. An all-white executive council controlled the movement, and a separate committee, also white controlled, was responsible for coordinating the “black work”. This situation would lead to many black secessions from the AFM resulting in the formation of African Initiated Churches, but the church would continue to have a large black constituency, who continued to exercise considerable autonomy in their local churches. As the AFM adopted the “daughter churches” approach to missions from the Dutch Reformed churches, eventually the AFM was divided into four main groupings: the white parent church, a large black daughter church, a coloured daughter church and an Indian daughter church.