To the church's rear is the Capuchin Monastery of St. John the Baptist, located at 210 West 31st Street across from New York Penn Station and Madison Square Garden.

[3] Kunze left with a portion of the congregation and founded the nearby Church of St. Francis of Assisi.

[3] The problems were so great with the board of trustees that, following the resignation of Kunze, the parish of St. John the Baptist was under interdict until 1845 when the Rev.

[1][3] Archbishop John Hughes laid the cornerstone for a new brick church on the site on March 14, 1847.

Lutz explained: "On account of the obstinacy of the parishioners this church was closed and the administration of the Sacraments prohibited by order of His Grace, November 24, 1851."

[1] Frey left in 1879 to serve as the Minister Provincial of the Capuchins friars in the United States, and moved to their headquarters in Calvary, Wisconsin.

Frey returned to the parish in 1888 and built the central bell tower in preparation for the church's Golden Jubilee held on January 18–19, 1891 and marked by Archbishop Michael Corrigan, Bishop Wigger of Newark, Archbishop-elect Katzer of Milwaukee and Abbott H. Pfraengle of Newark.

The church was re-dedicated on June 24, 1996, the feast day of its patron saint, by Cardinal John Joseph O'Connor, Archbishop of New York.

The church's organ and choir gallery, as well as a number of statues and stained-glass windows, were destroyed in a fire on January 10, 1997.

[1] According to bronze memorial plaques affixed to the wall of the narthex, for the 160th anniversary of the parish and the Great Jubilee Year of 2000, the bell tower was restored by funds provided by Antonio D'Urso and his wife Giovanna Parpo in 2000.

[8] The brown brick Capuchin Monastery of St. John the Baptist was built in 1974[9] in the Brutalist style.

[3] An additional floor was added to the rectory to accommodate the school and the Marist Brothers who were in charge of the boys.