Lowery was pastor of the Warren Street Methodist Church, in Mobile, Alabama, from 1952 to 1961. His career in the Civil Rights Movement took off in the early 1950s. After Rosa Parks' arrest in 1955, he helped lead the Montgomery bus boycott. He headed the Alabama Civic Affairs Association, an organization devoted to the desegregation of buses and public places. In 1957, along with Martin Luther King Jr., Fred Shuttlesworth, and others, Lowery founded the Southern Christian Leadership Conference and subsequently led the organization as its president from 1977 to 1997.