The FBCJ Sanctuary Organ, recently rebuilt by the Ouimby Organ Company of Warrensburg, Missouri, features numerous pipes from the church's older organ built by the famous American organ builder, E.M. Skinner, in 1940, as well as the organ from the Royal York Hotel, Toronto, Canada, built by Cassavant Organ Co. of Quebec. The church acquired the Casavant organ in 1989 and combined it with the Skinner organ for the new Sanctuary.

The Quimby organ now contains 155 ranks. A rank is a set of pipes with a certain sound quality, such as a trumpet or a flute. The instrument has approximately 9,000 total pipes housed in nine different rooms, three on the left and three on the right side of the baptistry and three in the back of the Sanctuary.

"Praise Him with the sound of the trumpet: praise Him with the psaltery and harp. Praise Him with the timbrel and dance: praise Him with stringed instruments and organs."
Psalm 150:3-4