In each section church feeling ran high, and when the war came, the churches supported the armies.

As the Federal armies occupied Southern territory, the church buildings of each denomination were turned over to the corresponding Northern body, and Southern ministers were permitted to remain only upon agreeing to conduct "loyal services, pray for the President of the United States and for Federal victories" and to foster "loyal sentiment." The Protestant Episcopal churches in Alabama were closed from September to December 1865, and some congregations were dispersed by the soldiers because Bishop Wilmer had directed his clergy to omit the prayer for President Davis but had substituted no other.

The ministers of non-liturgical churches were not so easily controlled.

A Georgia Methodist preacher directed by a Federal officer to pray for the President said afterwards: "I prayed for the President that the Lord would take out of him and his allies the hearts of beasts and put into them the hearts of men or remove the cusses from office." Sometimes members of a congregation showed their resentment at the "loyal" prayers by leaving the church.

But in spite of many irritations, both sides frequently managed to get some amusement out of the "loyal" services.