The present limestone Romanesque building, the third on the site, was built in 1890–91 to designs by Robert W. Gibson and added to the National Register of Historic Places in 1996.

[5] Almost uniquely among upper Manhattan's houses of worship, St. Michael's Church has been located on exactly the same site for two centuries.

The first building was a simple white frame structure with a belfry, built for pewholders of Trinity Church, Wall Street, who sought a more convenient place to worship near their summer homes overlooking the Hudson River amid the farms on what is now Manhattan's Upper West Side.

Thomas McClure Peters extended a missionary church in the racially integrated settlement of Seneca Village, demolished to make way for Central Park.

[6] In the 1850s the Rector's wife Mrs. William Richmond transformed the John McVickar house, formerly the center of a sixty-acre estate south of St. Michael's, for a Protestant Episcopal "home for abandoned women who found no hand outstretched to help them".

[8] The third and current building, influenced by the Romanesque and Byzantine styles and designed to seat 1,500 people, was dedicated in December, 1891.

[10][11] The present church was erected after an elevated railroad was built on Columbus Avenue absorbing the rural district into the growing city.

[9][12][13] In 1895, Louis Comfort Tiffany (1848–1933) was commissioned to design and install the seven great lancet windows representing St. Michael's Victory in Heaven, along with a marble altar.

Twenty-five years later, Tiffany's overall design scheme was completed with the Chapel of the Angels reredos mosaic depicting the Witnesses of the Redemption.

[14] After the church building was completed, seven windows were commissioned and installed showing "St. Michael's Victory in Heaven."

After the Civil War, St. Michael's provided space and financial support for the free Bloomingdale Clinic, District Nurse Association, Day Nursery and Circulating Library.