Though a Roosevelt organ was originally contracted for the Cathedral, building progress was slower than expected. The contracted instrument was subsequently placed in a church in Jacksonville, Florida. The Austin Organ Company installed the first large-scale organ of The Cathedral of All Saints, Opus 45. Between 1901 and 1903, the organ was temporarily installed on the ground level and subsequently removed and re-erected in the clerestory and triforium chambers as they were completed. Minor alterations took place during this period including reworking of the console. Interestingly, it was the first four manual instrument built by Austin, and featured their first 32' Open Wood stop.

In 1927, Austin was commissioned to enhance the organ and provide a new “All-Electric” console. Electro-pneumatic engines were supplied and attached to control the expression of the Great, Choir, Solo, and Swell divisions. A new generator was installed for the proper operation of the new console and two new electrically driven tremolos were installed. A pedal chest and pipes were moved form the second arch on the chapel floor level to the corresponding arch on the opposite side of the chancel. Additions and replacements were made to the organ’s stoplist. West End divisions were proposed, but never installed.

Due to failing mechanism and new trends in organ design, the Æolian-Skinner Organ Company of Boston was commissioned to completely rebuild the Austin instrument in 1956. Working within a restricted budget, the organ was recast in the “American Classic” style as Opus 1275 by G. Donald Harrison, using new pipework, in addition to used and re-worked parts from an E. M. Skinner instrument. Some stops from the old Austin were retained. Harrison supervised the installation of the new Great and Choir-Positiv pipework, windchests, action, and wind system prior to his death that year. The remainder of the organ was completed under the supervision of Joseph Whiteford. 

The Swell division is located in a chamber on the southeast corner of the crossing at the triforium level. It is comprised largely of materials from the E. M. Skinner Opus 724 formerly of St. Paul’s Chestnut Hill, Philadelphia. New Geigens, Mixture, and chorus reeds were provided. The Pedal division, located at the triforium level of the northeast corner of the crossing is comprised of some of the old Austin pipework from the original organ, notably the 32' Open Wood, along with a new 8' Principal unit, Mixture, and16' Reed unit. A high-pressure hooded Trompette harmonique, played form the fourth manual, is also located in this chamber. The Great and Choir-Positiv divisions are located on the ground level above the choir stalls. 

Austin Organs, Inc. has subsequently added to and modified the organ. In 1963 a new console replaced the old Austin Console from 1923. (Due to budget restraints, Æolian-Skinner did not provide a new console in the 1956 installation.) David A .J. Broom of Austin Organs, Inc. revoiced the Swell reeds and replaced the 2' Octavin, Hautbois, and Mixture in 1974. In 1986 the Antiphonal Organ and Trompette en Chamade, located in the west balcony, were given in honor of Dr. Lloyd Cast, long-time Cathedral Organist and Choirmaster.