A harmonium organ served The Church of St, Barnabas until 1893, when an Odell pipe organ was installed.  The Odell must have been a worthy instrument, as it was rebuilt in 1931 and served until 1955.  Then, the Vestry resolved that "the time has come to retire the organ to whatever pastures are reserved for retired and faithful organs," and a new organ, made by the firm of M.P. Möller, was completed in 1956.

This organ consisted of 15 ranks (1,006 pipes) with a two-manual console and pedal board.  Through the years, this instrument underwent several renovations and upgrades to overcome difficulties in its original installation, and to meet the demands of an increasingly sophisticated music program.

In 1984 the remnants of another Möller organ, part of which had probably been an Aeolian, were acquired from a church in Bayside, Queens.  Several new stops were added, the great division was exposed in the arch of the north transept, and the Bayside manual console was connected.

Shortly after these renovations were completed, there were serious problems with leaks in the church roof and around the central tower. To get to the root of the problems, all of the plaster in the interior tower area was removed, repairs were made, and the plaster replaced.  The Möller organ continued to play, despite continuing water damage and work on the church building.

By the late 1990s, the Möller was now more than 40 years old and in need of a major overhaul as a result of its age and the hard life that had befallen it.  At this time, the Bunaes family promised a major gift for the purchase of a new organ, and the Vestry voted to replace the Möller.

The American Classic Organ Company of Chester, Connecticut was selected to build the new organ.  Their design called for an instrument romantic in sound, with a color and grandeur in the English tradition.  It required minimal architectural changes in the church building, salvaged some of the best stops of the old organ, and incorporated a division on the west wall of the church.  Work began in the fall of 2000, and an inaugural recital was held in October, 2001 with Mr. Timothy Byram-Wigfield of Jesus College, Cambridge as the guest recitalist.

There are 2,181 pipes and an electronic supplement equivalent to another 1,043 pipes.  Five divisions are played on three keyboards and a pedal board.  There are more than 147 devices, including 83 draw knobs, to allow the organist control of the instrument.