In 1997, Moss moved to Augusta, Georgia, to take up the pastorate at Tabernacle Baptist Church, founded in 1885 as Beulah Baptist Church. During the Civil Rights Movement the church served as a local base for that movement. At the time Moss took over the church, it had 125 members, growing to 2,100 members by the time he left it in 2006, reportedly mostly through the inclusion of formerly unchurched young people. During his tenure, the church also undertook a major renovation of their historic building. In 2000, he published a sermon collection entitled Redemption in a Red Light District - Messages of Hope, Healing and Empowerment, consisting of sermons from his first year of ministry. He also periodically swapped pulpits with the pastor of the First Baptist Church of Augusta, where the Southern Baptist Convention was originally organized in support of slavery. In 2002, he was the first recipient of a prize, carrying a $25,000 stipend, for exemplary community service, evangelism and preaching. He had been nominated by the historian of the Chautauqua Institution in New York who considered him one of the best to have preached there. The prize is jointly awarded by three Presbyterian organizations; the Columbia Theological Seminary, the Presbyterian College, and the Peachtree Presbyterian Church of Atlanta, Georgia. During this period, Moss was a member of the Progressive National Baptist Convention as well as state and local Baptist organizations. Politically, he was a member of the NAACP and the Georgia branch of the Rainbow/Push Coalition founded by Jesse Jackson. He also served on the boards of the local United Way chapter and Augusta's black history museum, which is named after Lucy Craft Laney.
Moss received two job offers. One was to come to the Olivet Institutional Baptist Church in Cleveland, Ohio to succeed his father as pastor, the other to move to Chicago's Trinity United Church, a United Church of Christ church pastored by Jeremiah Wright, to become Wright's successor at the roughly 8,500-member megachurch. Moss says that after prayer and fasting, he felt God's call was for him to go to Chicago, and did so in 2006, initially as Wright's assistant. Early in 2007, Moss was one of four additional contributors to the book The Gospel Remix: Reaching the Hip Hop Generation by Professor Ralph C. Watkins of the Fuller Theological Seminary. That summer, Moss was one of several black ministers who gave eulogies at a mock funeral the NAACP put on for the word "nigger", where he described it as "the greatest child that racism ever birthed". Wright gave his last sermons as pastor on February 10, 2008. After some guest sermons, Moss took the pulpit on March 9. Senator Barack Obama and family were members of Trinity United, and on March 13, during his 2008 presidential campaign a controversy broke out over racially and politically charged sermons by retiring pastor Wright. While Obama's candidacy had brought attention to the church, this brought even more attention to it. Time magazine claimed that Wright was holding on to power and preventing Moss from fully taking over as pastor, citing unnamed sources within the church. The following week, Moss and Wright told the congregation that the accurate title for him is indeed "senior pastor elect" because has not yet met UCC requirements for being installed pastor of a UCC church, and is expected to meet those requirements in the fall of 2008. A UCC spokesperson had told Time that "it was hard to imagine that Moss wouldn't successfully complete the ordination process." In May 2009 Moss was installed as the senior pastor of Trinity. , Moss is a board member of The Christian Century.
