As mentioned above, the American Missionary Association planted numerous academies and colleges for those African-Americans freed from slavery by virtue of the South's defeat in the American Civil War. In some cases, former Union officers returned to territories they had conquered to aid the emancipated new citizens. Among those institutions still existing today are Fisk University (Tennessee), Atlanta University (now Clark Atlanta University, Georgia), Talladega College (Alabama), and Tougaloo College (Mississippi).

Alongside their activities in educating, many of the teachers who were often Congregational pastors, founded churches for the freed people. A large number of them were founded in the beginning, but only 15 still remain in the Conference today. AMA congregations in the southeast and south-central states joined with "Afro-Christian" churches in North Carolina and Virginia to form the Convention of the South in 1950; that body was dismantled to distribute the congregations into their proper UCC geographical jurisdictions, ending segregation.

In the early 2000s, the Conference undertook a program to commemorate the legacy of those congregations and the AMA, titled "Rekindle the Gift." The Rev. Joyce Hollyday, then Associate Conference Minister and a former associate editor of Sojourners magazine, wrote a book in 2005 examining the AMA's past and the existing congregations' recollections and hopes, titled On the Heels of Freedom: The American Missionary Association's Bold Campaign to Educate Minds, Open Hearts, and Heal the Soul of a Divided Nation, released by Crossroad Publishing.

The AMA also undertook educational and social work in the mountains of Tennessee and Kentucky during that period, operating several schools for Euro-American Appalachian youngsters, with some churches alongside them as well.