In 1878, shortly after the dedication of the Church of Good Shepherd, a new organ with two manuals and 15 rank was purchased from George S. Hutchings of Boston. The tracker action organ was located on the right side of the chancel. The console was attached to the organ case, with the congregation seeing the back of the organist. The case pipes, facing the congregation, were stenciled in bright colors to match the rest of the interior design. The nave had not been painted in its present "white" at this time.

This instrument was replaced in 1949 by a three manual, 27 rank instrument from the Aeolian-Skinner Company of Boston. By 1974, the organ needed substantial leather work and the console was replaced with a new three manual all electric action console. View specifications in detail of Aeolian-Skinner Opus 1095 and more history of Aeolian-Skinner and its organs.

In 1983, E. A. Kelley Associates of Salem, New Hampshire renovated and tonally revised the Chancel organ, increasing the size to 30 rank.

In 1988, the people of Church of the Good Shepherd decided that part of the bequest of the late Esther Harless would provide for a new console of four manuals and a Processional Division to be erected over the main doors at the West End of the church. E.A. Kelley Associates was retained to design and install a four manual console and a new Processional Organ. In order not to block the main doors to the church, an airlock inside the main doors had to be constructed. It is through this airlock that the congregation passes to enter the church. The airlock and new interior doors were completed during the summer of 1989 and provide the footing for the 23-foot tall Processional Division.

The walls of the airlock contain two large conductors used to bring the compressed air from the basement up to the processional organ as well as the electric current and electronic signals from the console located in the chancel. These signals are used to control the valves that allow each of 761 pipes to speak. The airlock is over constructed in order to kill all vibration from the opening and closing of the massive doors of the church. If this had not been done, any slamming of those doors would have caused the organ to go out of tune because the vibration would move the tuning collars on the organ pipes above. These tuning collars are visible if one looks carefully through the screens of the chancel organ at the top of each pipe. They are shiny and generally made of aluminum and are used to lengthen or shorten the speaking length of the individual pipes.

The gold pipes are original to the Elias & George Hook facade built in 1852 for the Freewill Baptist Church of Somersworth, New Hampshire (Town of Great Falls in 1852). Over a period of three years, all of the pipework for the processional organ was carefully collected to reproduce a sound similar to that which the Hook brothers would have created in the mid 1850’s. The pipework selected was constructed during the period 1845 to 1890 to produce the silvery sound typical of Hook’s work prior to 1865. The pipes came from locations in New York, New Jersey and Maine.

The brass horizontal Festival Trumpet was first used at a service on Thanksgiving Eve, 1989 and are one of two horizontal trumpets in the state of New Hampshire. The resonators are spun individually as are the real orchestral instruments. Each was manufactured by hand and was secured from Australia.

The new four manual console was completed and installed for Advent in 1988. Church of Good Shepherd is the only parish in the state of New Hampshire with a four manual organ. The console is essentially an Aoelian-Skinner design with the English organ feature having all couplers on draw knobs, thus there is no rail of rocker tablets over the 4^th manual, allowing organists under six feet tall to read music from the music rack.