In 1903, Archbishop John Cardinal Farley bought a house for $13,000 ($440,000 in current dollar terms) at 249 East 71st Street as a residence for Fr.

[4] This served until September 25, 1904, when the Knox Memorial Presbyterian Church at 250 East 72nd Street was purchased for $39,000 ($1,320,000 and refitted for the use of St. John’s congregation.

The building had been built 1887 to the designs of notable Protestant ecclesiastical architect Robert Henderson Robertson[2][3] "Among the paintings presented to the church are the "Three Marys at the Tomb of Christ" (valued at $10,000) by Albert Zimmermann and "St. John Nepomucene" by Alphonse Mucha.

The chime of ten bells was a personal gift to Father Prout from Christian Young, a banker and a Lutheran, and was rung for the first time at New Year's 1905.

Only St. John Nepomucene and St. Frances Xavier Cabrini remained open for regular Masses and other events.