In 1887, the Reverend Henry A. Moore, D.D., became the Pastor and in 1889 the 35th Street property was sold for $60,000 and the 48th Street edifice was purchased. Reverend Moore remained until 1892 when Reverend Dr. Ernest Lyons was appointed. New growth in the membership caused the congregation to move to 53rd Street on June 2, 1895 and the church was incorporated in 1896.

A new era began with the appointment of Dr. William H. Brooks in 1897. During his pastorate, the church flourished in both membership and worship attendance. Dr. Brooks' assistants included Dr. Frederick A. Cullen, Dr. Willis J. King, Reverend Richard A. Bolden, Reverend Albert J. Mitchell, Reverend Frank Robinson, Reverend Richard McCarthy and Reverend Rosa Hancock.

As an outreach of St. Mark's, new churches were organized in other parts of the city included Salem Methodist Episcopal Church and Brooks Memorial Church. During the pastorate of Dr. Brooks from 1897-1923 properties were purchased then subsequently sold to purchase a site facing St. Nicholas Avenue which cost $43,000. Ground breaking ceremonies were held on October 22, 1922. thus, the new home of St. Mark's was established and the dream of Dr. Brooks became a reality.

From 1923-1932 Reverend Dr. John W. Robinson was the Pastor of St. Mark's and under his leadership the cornerstone for the new building was laid on September 9, 1924 adnd dedication took place on the first Sunday of December 1926.

In 1932, Dr. Lorenzo H. King became the Pastor and was soon regarded as one of America's greatest orators. In 1939 when the three methodist bodies united the word "Episcopal" was deleted, making the church Methodist.

From 1940-1958, Dr. Samuel Sweeny served as Pastor. the messenger was introduced on Sunday , October, 6, 1940. During this period, St. Mark's had the largest congregation in the Northeastern Jurisdiction of the Methodist Church. During this time also, the renowned Stain Glass Windows were installed.

Dr. Charles L. Warren was appointed to suceed Dr. Sweeney in 1958. He served until 1964 when he was appointed Superintendent of the Metropolitan District of the New York Annual Conference.

In 1964, Dr. John J. Hicks became the Pastor. Under his leadership the 139th Street parsonage was purchased in 1966 and the mortgage was burned on Easter Sunday, April 11, 1971. He was also instrumental in the creation of the St. Nicholas Historical District. In 1968, the methodist church and the evangelical United Brethren Church merged, forming the United Methodist Church and later becoming St. Mark's United Methodist Church. After serving for nineteen years, Dr. Hicks died november 1983. Reverend Calvin O. Pressley served as interim minister for eight months.