The Records of the Brooklyn Division of the Protestant Council of Churches offer the history of a century of Protestant organizations originating from the Brooklyn City Tract Society, which was founded as a branch of the American Tract Society in 1829 to "promote the interests of evangelical religion, by the systematic distribution within the bounds of [Brooklyn], of religious Tracts published by the American Tract Society: and to aid that Society, with all surplus funds, in extending its operations." Originally focusing on the dissemination of religious literature and scripture, the Society soon expanded to offer religious services, and employed missionaries to extend their work throughout the City of Brooklyn. The Society's name was changed in 1858 to The Brooklyn City Mission and Tract Society, and in the same year its constitution was amended to reflect this change.

The Society continued to prosper under its new name, employing both men and women as missionaries, and made active efforts to reach out to the underprivileged, including mothers and children, especially recent immigrants. Much of the Society's work focused upon the idea of "American Christianity" with the hope of turning its wards into devout Christians and "reliable and helpful citizens." Each missionary was charged with the task of visiting every tenement in his or her district, distributing literature, and, if welcomed, establishing neighborhood prayer meetings.

In 1886, the Woman's Branch of the Brooklyn City Mission and Tract Society was formally organized. Known as the Women's Auxiliary from 1887 on, this division coexisted alongside the Society and "was to supplement the work of The City Mission, by taking up mission work to be done in homes among women and children." All Christian women were encouraged to join the Auxiliary, not necessarily to work as missionaries, but to lend their prayers, influence, and financial support to the cause of missionary work.

The Society sponsored many activities aimed at drawing persons away from vices such as alcohol and gambling. Activities sponsored by the Society included lectures, prayer meetings, bible classes, and a sewing school. The Society founded a "Floating Bethel" in 1893. This boat/meeting house was removed from the brothels and taverns of the waterfront and provided a space where sailors could come to read, write, rest, and pray.

In addition, the Society worked to "rescue the perishing," primarily through its City Mission Night Shelter for Homeless Men, which provided food, shelter, aid in obtaining employment, and religious services. The Society itself offered employment to many, running a broom factory and chair caning facility. These successful business ventures helped defray the costs of the Society's charitable work.

As the Society continued to expand, it focused less on the dissemination of literature. Missionary work had become the Society's primary function, and by 1906 it operated 16 mission stations in Brooklyn. The Society chose to change its name accordingly in 1929 to the Brooklyn City Mission Society. The bylaws were also amended, declaring the Society's objective as being "to promote interdenominational missionary interests in the Borough of Brooklyn and to minister to the spiritual and material needs of the unfortunate." Shortly after this change in 1932, the Brooklyn City Mission Society took on the work of the Brooklyn Federation of Churches. The Federation had been established in 1920 to bring all Protestant denominations and races together in a cooperative effort to promote Christianity through religious education, social service, court work, and other venues. The two organizations had operated side by side for many years, sharing a Secretary, Dr. Frederick M. Gordon, from 1926 to 1932. The Society again changed its name, this time to the Brooklyn Church and Mission Federation. The bylaws of the Brooklyn City Mission Society were amended in accordance with the restructuring to declare a twofold object: 1) "to unite the Protestant Churches of Christ in Brooklyn for the prosecution of work that can better be done in union than in separation, and to secure a larger combined influence for the churches in all matters affecting the religious, moral and social welfare of the people, so as to promote the application of the law of Christ in every relation of human life," and 2) "to promote interdenominational missionary interests in the borough of Brooklyn, and to minister to the spiritual and material needs of the unfortunate."

The Federation continued to operate as such over the next decade, working throughout Brooklyn to reach out to a large, diverse, and changing community. With the Great Depression, the church had to rethink its mission, focusing more on service to the community and providing aid to those in need. Outreach during this time included mothers' clubs, boys' clubs, parole and court work, civic affairs conferences, industrial relations conferences, and population surveys. The Federation also began to focus on church unity, as it observed that cooperative efforts would "produce greater strength and a more definite program and positive results."

In June of 1946, the Federation "voted to amalgamate its program and activities with The Protestant Council of the City of New York to become the Brooklyn Division of the Council." Although the Brooklyn Church and Mission Federation was not officially dissolved, the organization was now widely known as the Brooklyn Division of the Protestant Council of Churches. As such, the organization further shifted its focus to church unity and the future survival of the Protestant Church.

With the demographic changes of the early and mid-20th century, the face of Brooklyn Protestantism had changed greatly. At the turn of the century, Protestants made up more than one-half of Brooklyn's population. By 1950, Protestant Brooklynites had dropped to 19.5 percent of the total population. The increase in immigration of non-Protestant groups and the movement of the population to the suburbs led to a major decrease in the population of the Division's traditional Brooklyn base of white Protestants. By the later half of the 20th century, Protestants had become a religious minority within both the Borough of Brooklyn and the City of New York, causing the church to reevaluate its position within the community. The Division expanded its field of social services to include work with veterans, hospital and jail chaplaincies, interracial projects, peace activities, and economic justice programs. As the Division moved its focus towards social service and away from direct mission work, it strove to identify the church as an indispensable part of the community. It strove to promote unification especially with the growing African American Protestant community that made up nearly one-half of Brooklyn's Protestant population by 1963. The Division continued for the remainder of the 20th century to use its influence as a united body within the community to strive for social reform to assist Brooklyn's ever changing population.