All Souls Episcopal Church was established in 1859 but found its current home in 1908. All Souls offered services and programs to a growing African American congregation. By 1932 almost half of the congregation was black, and 200 black children attended the Sunday School. At the time, white residents resisted the changing population, and many predominantly white churches closed or moved. To curb this trend, the vestry discouraged the reverend from inviting black people into the church. After multiple failed attempts at this, and even chaining the doors, the vestry relented. The church was now open "to all the people in the neighborhood ... without distinction of race or color".

The building that houses St. Martin's Episcopal was erected in 1886. At the time, the church was called Holy Trinity Church, but that congregation moved to Inwood after a fire gutted the structure. Soon after, the Diocese of New York was given the building and christened it St. Martin. As Harlem gained a large West Indian population in the 1930s, the church soon became known as "The Carribean Church." St. Martin's served its community by advocating for the employment of Black people in stores along 125th Street. St. Martin's also established a credit union to help its members obtain mortgages. St. Martin's is best known for being one of the three churches in New York City with a carillon. These forty-two bells are currently out of commission because of water damage, but the church is accepting donations to bring the building back to its former glory.

Ephesus Seventh Day Adventist Church is a Gothic style building constructed in 1887 and designed by John Rochester Thomas for the Second Collegiate Church of Harlem. The facade's lower level shows carved monsters and a man with a mustache hides between the doors. A fire destroyed the church's original interior, but its truncated steeple, which was also impacted by the flames, can be seen for blocks along Malcolm X Boulevard. Booker T. Washington gave a sermon here and the Boys Choir of Harlem was founded here in 1968.

St. Andrew's Church has a Gothic Revival design from Henry Martyn Congden, St. Andrew’s Episcopal Church was built in 1872 and has been a New York City landmark since 1980. With a clock tower that is 125 feet. tall, it was the first Episcopal parish in Harlem. In 1942, the church discontinued its practice of renting pews, which opened the church to black parishioners.

Formerly St. James' Methodist-Episcopal Church, Metropolitan Community United Methodist Church has been a pillar in the community since its construction in 1871. Rembrandt Lockwood, the architect, gave the church rough brownstone walls and a tower supporting a 188-foot steeple. The population of the church shifted from white to mostly black in the early 1900s as African Americans began to move into the neighborhood. During the 1930s, the church became the center of controversy as the pastor at the time held a meeting with known Communists.

All Saints Church was once known as the "St. Patrick's of Harlem" because of its size and grandeur. The church is adorned with rose windows and a prominent bell tower. It was designed by architects Renwick, Aspinwall and Russell and opened in 1886. At the time, the parish was intended for the neighborhood's Irish immigrants, but as the population of Harlem changed, so did the congregation. All Saints School was run by the Christian Brothers of Ireland and the Sisters of Charity of New York. All Saints School was closed in January 2011 and, in the summer of 2017, the church was deconsecrated. The building was designated a city landmark in 2007.

The Abyssinian Baptist Church was completed in 1923. Designed Charles W. Bolton & Son, the building features stained glass windows and marble furnishings. The congregation of the church began in the early 1800s when Ethiopian seamen and African American parishioners protested segregated seating in Harlem churches. It is the third oldest Baptist church in America. By 1930, the church had 13,000 members and was an important site for gospel museum during the Harlem Renaissance. In 1989, Abbysinian was the first church to participate in the Harlem Week of Prayer and mobilized the support of people with AIDS and their families.

Mother African Methodist Episcopal Zion Church, also known as "Mother Zion" is the oldest African American church in New York City. The congregation was established in 1796 by African American members of the John Street Methodist Church. The John Street church was abolitionist, but still segregated sacraments and other religious practices. AME Zion was once referred to as the "Freedom Church" for its involvement in the abolitionist movement and was a refuge along the Underground Railroad. Sojourner Truth was a member of the congregation, while Harriet Tubman and Frederick Douglass were members at other AME Zions. Being pro-abolition marked Mother Zion as a target during a three-day anti-black riot in 1834. After moving spaces multiple times, Mother Zion settled in its current building in 1925. The neo-Gothic church was designed by George W. Foster Jr., one of the first registered African American architects in the United States. The church seats about 1000, and the vestibule houses several historical artifacts from the church's history.