A pipe organ for St. John's arrived late in 1827, and was in use by early 1828. It was upgraded in 1850, replaced in 1862, moved to the present location in 1912, and progressively extended and upgraded after that time, the most recent extension taking place in 2007.

Church organs are, of course, used to lead choral and congregational singing in services of worship, but are also showpieces in their own right, used for performances of world-renowned works by famous composers, at times by virtuoso organists. This has certainly been the case at St. John's.