The building and organ of South Congregational Church were both completed in 1866, the former building and organ having burned. J.H. Wilcox, later a prominent builder in his own right, regulated and tuned the organ as a Hook employee, and played the dedication recital on June 22, 1866.

The organ remained unchanged until the turn of the century when H.C. Harrison of Portland, Maine removed the Great 2 2/3' Twelfth in favor of the Swell Clarinet and placed a Salicional and Aeoline in the Oboe/Bassoon and Violina spot respectively. A Voix Celeste was installed in the former Clarinet spot. The Great upper work was softened.

The Andover Organ Company restored the instrument in 1982 and restored the Clarinet to the Swell, Installed a 2 ²⁄₃' Twelfth from E. & G. G. Hook & Hastings Opus 831 on the Great; removed the Salicional, Aeoline and Voix Celeste from the Swell and installed a Violina from E. & G. G. Hook, Opus 470 and an Oboe/Bassoon from E. & G. G. Hook Opus 371. All original voicing was carefully restored as was the action and windchests. The organ was returned to its original pitch. The work was under the direction of Robert C. Newton, Vice President of the Old Organ Department.