Two other great Southern churches, the Presbyterian and the Methodist Episcopal, grew stronger after the Civil War. The tendency toward reunion of the Presbyterians was checked when one Northern branch declared as "a condition precedent to the admission of southern applicants that these confess as sinful all opinions before held in regard to slavery, nullification, rebellion and slavery, and stigmatize secession as a crime and the withdrawal of the southern churches as a schism." Another Northern group declared that southern ministers must be placed on probation and must either prove their loyalty or profess repentance for disloyalty and repudiate their former opinions. As a result several Presbyterian bodies in the South joined in a strong union, to which also adhered the synods of several Border States.

The Methodist Episcopal Church, South, was confronted with conditions similar to those which prevented the reunion of the Presbyterians. The Northern church, according to the declaration of its authorities, also came down to divide the spoils and to "disintegrate and absorb" the "schismatic" Southern churches. Already many Southern pulpits were filled with Northern Methodist ministers placed there under military protection; and when they finally realized that reunion was not possible, these Methodist worthies resolved to occupy the late Confederacy as a mission field and to organize congregations of blacks and whites who were "not tainted with treason." Bishops and clergymen charged with this work carried it on vigorously for a few years in close connection with political reconstruction.