The organ in the present building was originally built by the Ernest M. Skinner Company of Boston, Massachusetts in 1918 and incorporated many ranks from instruments in the previous church by George F. Hutchings of Boston and J. H. and C. S. Odell of New York. A precedent was laid for the design of the Skinner organ in the Hutchings instrument of 1893 and 1896. It had several divisions in the chancel and rear gallery and was played through electric action from a movable four-manual console in the chancel. Much acclaimed in its day, this double organ was played by the famous conductor Leopold Stokowski who came from England in 1905 to become organist and choirmaster of St. Bartholomew's. Several years earlier, on New Year's Day 1901, the famed organist Edwin Lemare made his American debut on this instrument.
The Skinner organ in the new Park Avenue church consisted of nine divisions with pipes placed in the chancel and west gallery. The mechanism was entirely new, and the chests were of the electro-pneumatic Pitman type, perfected by Skinner. All divisions played from a four-manual console in the chancel. It was one of the firm's most prestigious instruments at the time.