The first instrument used at All Saints' was a harmonium borrowed for the first service held in the partially completed, roofless west-end in 1861. In 1864, a cabinet organ was purchased for £63. In 1868, a pipe organ was purchased, which was extended by George Fincham in 1872 by the addition of a Choir Organ. This organ was later sold to St Andrew's, Clifton Hill.

The current organ was installed in 1924 and dedicated on 12 October, the organist being Dr A E Floyd. This organ was built by Roberts Ltd of Adelaide, as a three manual instrument with 45 speaking stops.

In 1982 a major rebuild was undertaken by Australian Pipe Organs Pty Ltd, with conversion to electro-pneumatic action and tonal improvements including the addition of mixture ranks and the conversion of the Great Tromba to a solo rank on its own higher pressure wind chest. In 1998, the Trumpet 8' was added to the Great.

The organ is maintained by Australian Pipe Organs Pty Ltd.