In the early 1800s, Black Charlestonians -- both enslaved and free -- were permitted to attend white-dominated Methodist churches, but only under strict control: segregated galleries, separate services held in basements, and white oversight of all worship. In 1818, after white leaders of Bethel Methodist authorized construction of a hearse house over the church's Black burial ground, nearly 2,000 Black members walked out of Charleston's three Methodist churches in protest. Church leader Morris Brown led them to found what became the Hampstead Church on Reid and Hanover streets. The new congregation affiliated with the African Methodist Episcopal Church, the first independent Black denomination in the United States, founded in 1816 in Philadelphia by Richard Allen. South Carolina law required a white majority in any congregation and prohibited Black literacy. Charleston officials arrested 140 Black church members in 1818 and sentenced eight leaders to fines and lashes. Police raided the church again in 1820 and 1821.

In June 1822, Denmark Vesey, one of the church's founders, was implicated in an alleged slave revolt plot. Vesey and five other organizers were convicted and executed on July 2 after a secret trial. The city conducted additional trials over the following weeks, ultimately executing more than 30 men and deporting others from the state, including Vesey's son. A mob of angry whites burned the original Emanuel AME church to the ground. Morris Brown was imprisoned for months, though never convicted. Upon his release, he fled to Philadelphia. After the Nat Turner slave rebellion in 1831, Charleston outlawed all-Black churches entirely in 1834. The AME congregation did not dissolve. It met in secret for more than three decades, worshipping underground until the end of the Civil War in 1865. That thirty-year span of clandestine faith is central to understanding Mother Emanuel. The congregation survived not because authorities permitted it but because its members refused to let it die.

After the war, AME Bishop Daniel Payne installed the Reverend Richard H. Cain as pastor. The congregation rebuilt the church between 1865 and 1872 as a wooden structure under the direction of architect Robert Vesey -- the son of Denmark Vesey, the executed church co-founder. That lineage was no coincidence. It was a statement. Cain went on to serve in the South Carolina Senate from 1868 to 1872 and then in the U.S. House of Representatives as a Republican congressman, establishing a tradition of Mother Emanuel's pastors serving in political office that would continue into the 21st century. The current brick and stucco building was designed by leading Charleston architect John Henry Devereux and completed in 1892 on Calhoun Street. The church was deliberately built on the north side of what was then called Boundary Street -- Blacks were not welcome on the south side. Today, Mother Emanuel retains one of the few well-preserved historic church interiors in the area, with the original altar, communion rail, pews, and light fixtures still intact.

Mother Emanuel's role in the civil rights movement was a continuation of its founding purpose. In March 1909, Booker T. Washington spoke at the church to a biracial audience that included the mayor of Charleston. In 1962, Reverends Martin Luther King Jr. and Wyatt T. Walker of the Southern Christian Leadership Conference urged the congregation to register and vote. In 1969, Coretta Scott King led 1,500 demonstrators to the church in support of striking hospital workers; they were met by bayonet-wielding members of the South Carolina National Guard, and 900 were arrested along with the church's pastor. Through the 20th century, Mother Emanuel was where Charleston's Black community gathered not only to worship but to organize, to resist, and to demand the rights that the nation's founding documents had promised and its institutions had denied.

On the evening of June 17, 2015, a 21-year-old white supremacist joined a Bible study group at Mother Emanuel. After sitting with the congregants for nearly an hour, he opened fire, killing nine people. Among the dead were senior pastor and South Carolina State Senator Clementa Pinckney, along with Cynthia Hurd, Depayne Middleton-Doctor, Sharonda Coleman-Singleton, Susie Jackson, Myra Thompson, Tywanza Sanders, Ethel Lance, and Daniel Simmons. The shooter was convicted of 33 federal hate crime and murder charges in December 2016 and sentenced to death in January 2017. The church, on its own website, refers to him simply as "the stranger." Four days after the massacre, Mother Emanuel held its regular Sunday service. The pews were full. The congregation sang, prayed, and worshipped in the same sanctuary where their friends had been murdered. It was what Mother Emanuel had always done: endure, rebuild, and open its doors again.