Saint Clement is fortunate to have two fine mechanical action pipe organs in the upper church. The main organ in the gallery, and a small portable organ in the front of the church.

The Casavant Organ

Built in 1983, the main organ was built by the Canadian firm of Casavant Frères in St. Hyacinthe, Québec, and installed in the church's rear gallery. The organ's tonal design was conceived by Jean-Louis Coignet, and final voicing was done by Yves Champagne and Michel Jacques.

The organ has mechanical stop action and suspended mechanical key action, and comprises twenty stops (27 ranks/1396 pipes) over two manuals and pedal. Manual compass is 56 notes, and pedal 30 notes. The hand-made casework is solid oak; manual natural keys are made of ebony, with sharps of rosewood capped with ivory; pedal naturals are made of maple, with sharps of rosewood. The façade pipes are 70% polished tin, and the organ's wind pressure is 80mm throughout. The Casavant organ was originally tuned in an unequal temperament modified from Werkmeister III. In 2008 the temperament was changed to Kellner. 

The Cassavant organ specification is as follows:

Montre 8
Flûte à cheminée 8
Prestant 4
Flûte conique 4
Doublette 2
Fourniture V
Douçaine 16
Trompette 8
POSITIF (expressif)
Bourdon 8
Prestant 4
Flûte à fuseau 4
Nasard 2 2/3
Quarte de nasard 2
Tierce 1 3/5
Cymbale IV
Hautbois 8
Soubasse 16
Octavebasse 8
Octave 4
Bombarde 16

The Taylor & Boody Organ

In 2005 Saint Clement acquired a magnificent five-stop portative organ built by Taylor & Boody Organbuilders of Staunton, Virginia. This small movable pipe organ is used primarily in the front of the church to accompany cantors, choirs and instrumentalists during the liturgy, as well serving as a complement to the larger main organ in leading hymn singing and other service music. The Taylor & Boody organ is also used as a continuo instrument in concerts with orchestra.

Constructed by hand from the finest woods and metals, the instrument was built according to historic organ building principles, with a keyboard of boxwood and ebony, and a case of superbly carved white oak. The organ stands about 3-1/2 feet tall, 2 feet deep and, 3-2/3 feet wide, and weighs about 200 pounds. Manual compass is 51 notes. The

case was designed to reflect many of the symbols and architectural elements of the Saint Clement church building, and features beautiful hand carvings on three sides.

The most essential part of any organ is its sound, and this one is no exception — the sounds in the Taylor & Boody organ range from sweet and gentle to brilliant and sparkling. Each sound has been voiced with utmost care, and even with only five stops, the combinations are varied and plentiful. The instrument's pipework features tuning sleeves, permitting the organ to be tuned in a variety of temperaments. In addition to several large instruments, Taylor & Boody have built many similar continuo organs in recent years, most notably for Harvard, Yale and Rutgers Universities, and for Saint Thomas Church in New York City.

The Taylor & Boody organ specification is as follows:

Gedackt 8 (wood)
Blockflöte 4 (wood)
Principal 2 (metal)
Quinte 1-1/3 (metal)
Sesquialtera II (metal, from middle c)

The keyboard is transposable to two pitch levels: A-440 and A-415. A-440 is the standard pitch at which most music today is performed. A-415 is used primarily with period instruments in early music.