During 1874–1884, the complex was the original home of the Presentation Sisters in the northeastern United States, and enrollment grew to become the largest parochial schools in New York.

At the suggestion of the pastor, John A. Gleeson, the Archdiocese sold the parish properties in exchange for a new church, school, convent, and rectory on 34th Street.

The office of Napoleon LeBrun & Sons was responsible for the construction of the new complex, which involved the salvage and re-use of the altar, organ, stained glass windows, and limestone facade.

[5] The church underwent renovations in 2019, including a new red oak baldachin designed by Patrick Alles, which received the McKim, Mead & White Award for Craftsmanship and Artisanship from the Institute of Classical Architecture and Art.

[6][7] St. Michael's parish and schools have produced hundreds of priests and religious vocations, including at least two bishops: Daniel Joseph Curley and Thomas John McDonnell.