In 1858, Tappan was the Treasurer of the AMA. Under the leadership of President Lawrence Brainerd, Tappan, Foreign Corresponding Secretary Rev. George Whipple, and Home Missions Corresponding Secretary Rev. S. S. Jocelyn, the AMA opposed the long-established and powerful American Board of Commissioners for Foreign Missions and American Home Missionary Society because of what the AMA alleged was their complicity with slavery. During and after the American Civil War, Tappan and his brother Arthur worked from New York with the AMA on behalf of freedmen in the South. In postwar efforts, it led the founding of numerous schools and colleges for freedmen, the historically black colleges and universities (HBCU).