A small pipe organ was installed by Samuel Warren at the end of the nineteenth century, which was subsequently rebuilt and enlarged on three occasions by Casavant Frères. In 1969, the tonal scheme of the organ was significantly altered under the guidance of former Organist and Choirmaster, Godfrey Hewitt. Several new stops were added at this time and the console was made movable so that recitalists could better be seen by audiences.

In 1997, under then-Director Frances MacDonnell’s supervision, the console was equipped with Solid State Logic, and a new “en chamade” trumpet was added in the rear gallery.  However, by 2007, the organ was determined by independent professional assessments to be urgently in need of repairs. Following this advice, Parish Council Executive recommended replacing the organ with a new pipe instrument at such future time as independent sources of funding are found and the Cathedral's debt is retired.

In the interim the Cathedral purchased in 2009 a digital instrument from Rodgers Organs Canada. In purchasing this instrument, Parish Council Executive emphasized that “this does not preclude any long-term or permanent organ replacement options”. With fifty-four stops (and a significant number of alternative voices), the organ has proven a reliable and flexible vehicle for choral accompaniment, service playing and recitals. 

The Cathedral also possesses a small continuo organ built by Karl Wilhelm of Mont St. Hilaire, Quebec.