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.

The "Christian Connection," a group of churches generally associated with the Restorationist movement, emerged in the Chattahoochee River valley of western Georgia and eastern Alabama in the mid-19th century with a number of congregations espousing the "five points" of Christian unity. This group later founded Southern Union College in Wadley, Ala., now a part of the Alabama state junior/community college system. Most of their congregations were located in the open country and reflected the population's general preferences for Wesleyan/Arminian theology and revivalism, typical of the rural South generally. Two institutions related to the Christian tradition, Elon College (now University) and Elon Homes for Children, both located in North Carolina, received considerable financial support over the years from these churches.

Although a number of the churches in this group initially supported the UCC and the Conference in the 1960s and 1970s, most later reconsidered those commitments, in large measure due to increasing theological and political disagreements (instigated in part by pastors who came to those churches from other traditions) with those congregations in the metropolitan areas, especially over the issue of homosexuality. Only three congregations from this tradition are known to remain affiliated with the UCC, but remnant members of some of the defecting congregations formed a new one in 2006, located in Chambers County, Ala.

Among Euro-American residents of Alabama and Georgia in the late 19th-century, some members of the Methodist faith began opposing the rise in power of the superintendents who began calling themselves "bishops." They desired local control, particularly the ability to call their own pastors, rather than have them appointed, without their consent. When some of these individuals and churches left the main Methodist body, a few of them joined the Congregational fellowship in the 1890s, recruited by agents of the American Home Missionary Society seeking a presence for Congregationalism in the South. Pockets of strength for this movement included northwestern, central, and southeastern Alabama; west central, south central, and northeastern Georgia; and the "Panhandle" region of northwestern Florida.

According to the book Southern Congregational Churches, self-published by UCC pastor and amateur historian Richard Taylor in 1994, the Congregational Methodist-heritage churches usually espoused extremely individualistic views, frequently opposing missionary societies and Sunday schools, very much akin to the Primitive Baptists and the Churches of Christ, two other groups that developed in the rural South during that same time. Therefore, they never developed close relations with Congregationalists in other parts of the U.S., since these stances were almost entirely opposite those honored in Congregational churches in most other regions, where education and mission work were held in very high regard.

Those churches not participating in this affiliation move (including some who recanted their earlier decisions to join the Congregationalists) constituted the Congregational Methodist Church, a small evangelical denomination headquartered in Mississippi. As with the Christians, nearly all of the Congregational Methodist-derived congregations eventually left the UCC over a period from the 1960s until the early 1990s, largely over the same theological and cultural disputes with denominational and Conference leadership. Only three of them remain in the UCC as of 2007, two in Alabama and one in Georgia.

Probably the most active of the several groups that formed the Southeast Conference were those Congregational churches founded, mostly in the early 20th century, as theologically liberal, socially tolerant alternatives to the dominant expressions of Southern Protestantism, namely the Baptists, Methodists, and Presbyterians. Migration of Northern Congregationalists to the South helped start several churches, often in close proximity to Euro-American colleges and universities (e.g., Vanderbilt University, Piedmont College). In a few cases, however, parts of established congregations withdrew to form Congregational churches in protest over doctrinal rigidity and/or lifestyle restrictions. These churches were located in cities such as Atlanta and Nashville; subsequent UCC new church starts in the Conference (e.g., Huntsville, Ala. and suburban Atlanta) have generally modeled themselves after this group, which has provided the dominant ethos to the UCC nationally ever since its inception.

By the mid-20th century, these became among the first Euro-American churches in the region to protest racial segregation and deeply involve themselves with advocating on African-Americans' behalf. And, since the 1990s especially, several of these have become ardent supporters of gay rights and have endorsed a stance to refrain from denying membership to those professing alternative sexual orientations, a move against the dominant social attitudes in the region.

Generally speaking, congregations in this group are the most aware of, and loyal to, the larger UCC, and are usually the most generous givers to Conference and national work. One reason for this is a high number of them have a significant percentage of members who previously belonged to UCC congregations elsewhere in the U.S., members who tend to be not only more aware of the denomination's heritage and program, but translate that knowledge into active support.

In the late 19th century, churches in the above three categories formed state conventions in Alabama, Georgia, Kentucky, and Tennessee. The Alabama convention included churches in northwestern Florida, and the Tennessee convention included African-American churches prior to 1915. Because none of the conventions was able to support a full-time superintendent (now known as conference minister, in the UCC) to itself, the conventions united in 1949 and became the Southeast Convention, with only minor adjustments to the territorial boundaries. This body had three superintendents:
The Rev. Dr. David W. Shepherd, 1949-1952
The Rev. Erston M. Butterfield, 1952-1957
The Rev. James H. Lightbourne, Jr., 1957-1965

After the Civil War, a group of settlers from Germany came, via Cincinnati, Ohio and Louisville, Ky., to northern Alabama and founded the town of Cullman, starting a church of the unionist Evangelical tradition; German immigrants to nearby Birmingham established a sister congregation there also. Meanwhile, some farmers from Switzerland, facing grave land shortages, responded to an advertisement in the 1870s offering farmland in Tennessee. Despite the fact that it amounted to a scheme to populate mountainous, infertile areas, the farmers (many of them dairymen) persevered, and some established Reformed parishes along the lines of the Swiss Protestant faith, several (only one survives) in southern middle Tennessee, and one in Nashville. As of today, only the Tennessee congregations remain affiliated with the UCC; the Alabama churches withdrew, led out in both cases by fundamentalist pastors in the same manner as some Christian- and Congregational Methodist-heritage congregations have been.
1966 to the Present

In large measure, the Southeast Conference was the product of the determination of national and regional leaders to comply with the mandate from the denomination's General Synod to align inter-church relationships according to geography instead of racial and ethnic groupings inherited from the past. Because of differences among the churches and pastors in the Euro-American Southeast Congregational Christian Convention regarding the denomination's involvement in the Civil Rights movement, the Southeast was one of the last regions in the country where all UCC congregations within its boundaries came together into one judicatory. Much of the immediate controversy was precipitated by a resolution from the Fourth General Synod, meeting in Denver, Colo. in July 1963, that called for the termination of financial support for churches and institutions that practiced racial segregation, and encouraged other UCC entities to do likewise. Only the adjoining Southern Conference, consisting of churches in North Carolina and Virginia, experienced difficulty organizing because of this, other than the Southeast.

After a failed attempt in 1964, the Southeast Convention, by a vote of only 54 percent, agreed to receive churches from the Congregational Christian (UCC) Convention of the South (African-American) and the southernmost congregations of the South Indiana Evangelical and Reformed Synod (Indiana-Kentucky Conference, UCC). This occurred at the Convention's annual meeting on April 24, 1965 at Central Congregational Church in Atlanta, Ga. The agreement brought the Conference officially into being on January 1, 1966. On April 23 of that year, meeting at First United Church (Evangelical and Reformed), Nashville, Tenn., annual meeting delegates adopted a constitution, consummating the process. The first officers of the new Conference were the Rev. Frederick A. Meyer, pastor, Central Church, Atlanta, moderator; Mr. J. Hubert Richter, member, St. John's (Evangelical Protestant) UCC, Cullman, Ala., vice-moderator; Miss Ellen Hull, member, Langdale Congregational Christian Church, Valley, Ala., recording secretary; Leslie Beall, member, Central Church, Atlanta, treasurer. The board of directors consisted of association representatives and chairpeople of commissions elected at large; initially, the Conference consisted of nine associations, but that number dropped to six by the early 1970s due to several of them merging.

Meanwhile, Conference staff and leaders, espousing the predominantly liberal outlook of the denomination, made extraordinary efforts to encourage churches to pursue aims such as advocating for peace in Vietnam, improved racial relations, and formulating a more articulate and relevant faith for the needs of the younger generation. This was particularly remarkable because Conference ministers, and associates, undertook these aims in addition to the daunting task of servicing the needs of churches spread over a seven-state region, which entailed much time and expense in travel and meetings distant from the Atlanta headquarters. Some churches were quite enthusiastic about all of these programs, engaging in experimental ministries and worship; others, mostly those outside the major metropolitan areas, resisted what they saw as an intrusion upon their traditions and autonomy, and these gradually began keeping to themselves, often only supporting their associations or customary benevolences. By the 1990s, many congregations simply decided to withdraw and form their own groupings or, just as often, become totally independent, a trait increasingly noticeable also among recently-established churches of fundamentalist or charismatic persuasion in the region. Those moves reduced the six associations down to the present three.

As with most UCC conferences, most of the Southeast Conference's current congregations antedate the 1957 union that formed the denomination. Until about the late 1990s, the Conference was either financially unable to support significant church expansion or experienced great frustration and lack of success on those projects it did enter into. Most of these have been centered in the metropolitan Atlanta area, where demographic experts have perceived the greatest patterns of growth. Even more problematic was the overweening fact that the Conference was dependent for many years on national subsidies simply to operate on a "maintenance" mode, let alone venture into expensive church building programs. Of course, the denomination was hindered by its lack of name recognition in the South (or, worse even, its confusion with the Churches of Christ, an entirely different evangelical Protestant tradition).

But, after years of decline and loss of disgruntled churches (which were mostly located in rural Alabama and Georgia), the Conference began to turn a corner in the 1990s, as it made an intentional effort to market its peculiar blend of evangelism and social service to both its existing congregations (through renewal programs) and especially individuals and churches disaffected from their historic traditions (e.g., Baptists, Methodists, Presbyterians, and non-denominational predominently-gay groups). The Conference, and some of its churches, has recently made particularly effective use of the UCC "God Is Still Speaking," branding campaign.