The congregation began in 1838 as Union Bethel A.M.E. Church, an offshoot of the larger African Methodist Episcopal denomination founded by Richard Allen in Philadelphia in 1816 - the first independent Black Protestant denomination in the United States. Washington in 1838 was still a slave-holding city; the District would not abolish slavery until 1862. The first Union Bethel building was modest, serving a free Black community that lived in the spaces the city's segregation allowed. In 1880, Bishop Daniel Payne sent the Reverend John W. Stevenson to lead the building of a new sanctuary worthy of what the congregation imagined itself becoming. The cornerstone was laid in September 1881. Stevenson, as it turned out, was a polarizing pastor with high salary demands, and the congregation removed him before the building was finished. Architect George Dearing completed the work. The new church was dedicated on May 30, 1886. The congregation reorganized under the new name: Metropolitan African Methodist Episcopal Church.

According to the church, Metropolitan AME stands on the oldest continuously Black-owned property in the original ten-mile-square District of Columbia. The building - a substantial Victorian Gothic sanctuary at 1518 M Street NW - has occupied the site since 1886. The congregation has held the title without interruption since the construction. In a city whose history of property ownership has been continuously reshaped by segregation, eminent domain, urban renewal, and gentrification, the Metropolitan AME building's unbroken Black ownership is itself a historical artifact. The building was added to the National Register of Historic Places in 1973. The congregation has long called itself the National Cathedral of African Methodism.

On February 20, 1895, Frederick Douglass died at his home at Cedar Hill in Anacostia. His funeral was held at Metropolitan AME on February 25. Douglass had been the most prominent Black American of the nineteenth century - abolitionist, orator, autobiographer, presidential advisor to four presidents - and the church was the natural site. The body lay in state at the church before the service. Black schools across Washington closed for the day so children could attend. One hundred ten years later, when Rosa Parks died in Detroit on October 24, 2005, her body was flown to Washington for a series of memorial services. After lying in honor at the U.S. Capitol Rotunda - the first woman ever to receive that distinction - she was eulogized at Metropolitan AME on October 31. Between those two funerals, the church hosted countless others - civil rights leaders, federal officials, congregants whose names did not make the national news. The same pulpit has spoken into the same air for one hundred and forty years.

In May 2010, the National Trust for Historic Preservation added Metropolitan AME to its list of America's 11 Most Endangered Places. Water damage and structural deterioration required an estimated $11 million in repairs. The Obamas attended services there on inauguration mornings. Restoration work continued through the 2010s. In December 2020, after President-elect Joe Biden's victory but before the January 6 storming of the Capitol, supporters of the outgoing president held a series of rallies in Washington. On December 12, marchers tore the church's Black Lives Matter banner from its fence and burned it. Proud Boys leader Enrique Tarrio was arrested and charged with destruction of property. The church sued Proud Boys International, LLC, and Tarrio personally on January 4, 2021. Neither responded. In June 2023, D.C. Superior Court Judge Neal E. Kravitz imposed civil penalties of more than $1 million on the Proud Boys and four members - Tarrio, Joe Biggs, Jeremy Bertino, and John Turano - citing what he called hateful and overtly racist conduct.

On February 3, 2025, the case escalated. Judge Tanya Jones Bosier issued a $2.8 million default judgment that included transferring the rights to the name Proud Boys and the group's trademarks to Metropolitan AME Church. The Proud Boys had lost their own name to the church they had attacked. Less than a year later, in January 2026, the church announced a new project on the parcel behind the sanctuary: micro-apartments for homeless veterans. Church leaders told The Washington Post the plan was in the concept stage and three to five years from completion. The congregation had buried Douglass and Parks. It had recovered its banner and acquired its attacker's trademark. Now it was preparing to house veterans on the same block where the cornerstone had been laid 145 years earlier. The church's name - Metropolitan, meaning a city's principal cathedral - was beginning to feel less like an aspiration than a description.