[7] A fire was attempted on the building on June 27, 1846 but was detected before any major damage was caused,[8] and a $200 reward was offered by the Mayor of Brooklyn for conviction of the perpetrators.

[13] In 1881, an anonymous donor provided funding for a new chapel and Sunday school building behind the main church edifice, on Vanderbilt Avenue.

A major fire in November 1887,[16] following all of this expansion[17] and caused by a defective furnace duct,[18] resulted in the destruction of the organ and altar as well as the chancel of the original church;[18] the original building remained intact in spite of damage, however, and continued to be used for Sunday services while a new Sunday school building and parish hall were built.

[19] The church's current building at 520 Clinton Avenue in Brooklyn, New York was built in 1888–91 and was designed by John Welch[20] in the Romanesque Revival style.

[20] A major fire in 1914 destroyed the interior of this building and caused sections of the roof to collapse,[26] but the outer walls remained intact.

[28] Following the March 1914 fire, the church was reconstructed using the outer walls of the former building, largely along the same design as the original but with an enlarged Sunday school and redesigned parish hall.

The building remained under heavy scaffolding for the following year[29] and reopened on September 19, 1915 in time for re-consecration on October 19, 1915.

[30] The organ was rebuilt in Hagerston, Maryland, and was designed to be the largest in the city,[30] with four manuals and sixty stops.

[37] In 2018, the church began work to sell air rights for construction of a nearby residential high rise, with proceeds from the sale paying for facade reconstruction and other repairs and improvements on the aging building in keeping with its Landmark status.

[45] By January 1866, a new organ had been installed and a concert was held with the choir of Trinity Church, New York, to dedicate it.

[20] While this merger is credited to decreased attendance and shifting neighborhood populations,[54] St. Matthew's Episcopal Church had also been embroiled in deep public controversy after its former rector, William S. Blackshear, stated explicitly in local press that the church wanted to remain white and was not interested in attracting any people of color from the neighborhood's changing population.

Blackshear's vestry stood by this opinion,[58] he was deeply criticized by both the bishop of the Diocese as well as by William Pickens[58] and James Weldon Johnson[59] of the National Association for the Advancement of Colored People.

[79] In 1853, a proposal was made and adopted to immediately cease interment of remains in the church vaults, for public health reasons.