Second Presbyterian houses two very fine pipe organs. The Sanctuary contains an 86-rank instrument built by the Æolian-Skinner Organ Company of Boston, Massachusetts (Opus 1490), installed in 1968 and renovated by the Schantz Organ Company in 2003. The organ of Milner Chapel was built by Casavant Frères of Quebec and consists of 2 manuals and 17 ranks, installed in 1974.

The Sanctuary organ is designed to make possible the performance of varied organ literature without undue stylistic compromise yet at the same time provide for the flexibility necessary for church services. It consists of six divisions: Great, Swell, Positiv, Choir, Chancel, and Pedal, and contains almost 5,000 pipes. The instrument may be controlled from two consoles, the main console of four manuals in the rear gallery, and the two-manual console in the chancel. The Chancel organ is also playable from the fourth manual of the gallery console. Resources of the gallery organ, expression shades and some combination pistons may be controlled from the chancel console. Thus the organist can accompany congregational singing from either position.

The Sanctuary also houses a 9-foot Model D grand piano custom-built for Second Presbyterian by Steinway and Sons in 2000.