The first console installed was a used, 4-manual, Austin stopkey console from Cleveland, Ohio. That console was replaced by the console from the 4/91 Aeolian-Skinner Op. 1399 that had been installed at the Cathedral of of St. Philip, Atlanta, Georgia, in 1962.

On Sunday, November 21, 1999 the gallery organ was blessed during the parish liturgy by Msgr. Michael F. Groden, Pastor of St. Cecilia Parish. It was dedicated in concert by organist Richard J. Clark on November 22, 1999, the Feast of Saint Cecilia.

Soon to follow was the installation of an antiphonal division of seven ranks, located near the front of the church, underneath the Saint Cecilia Window. Built in the 1960s by Robert Noehren, it was removed from St. Ignatius Episcopal Church in Antioch, Illinois. Reconstruction began in July 2000 by Adam Mittleman and Timothy Smith. Its inaugural liturgy was on the Feast of the Assumption, August 15, 2000. Soon after, Smith and Gilbert began reshaping its tonal design to tailor the organ to St. Cecilia Parish-s very specific liturgical needs. Furthermore, part of this retailoring included extensive wiring by Allen Taylor making the organ playable from both its own 2 manual console, and from the 4 manual console in the gallery. An 1850 W. B. D. Simmons case was refurbished by Andrew Smith of Cornish, New Hampshire and was installed in October of 2001. The completed Antiphonal Organ was dedicated in concert by organists Timothy E. Smith and Richard J. Clark on November 18, 2001.