The first pipe organ was installed in Trinity Church in February 1914. It was a gift of Mr. Nathan Reed in loving memory of his wife Elizabeth Smaling Reed, and of Andrew Carnegie, the steel magnate of Pittsburgh who was a part donor. Elizabeth Reed was the accompanist for the then Trinity Glee Club, and that picture is on display in the church narthex. Prior to this organ being installed, a manual pump organ that was located in the front of the chancel area, in both the 1873 church and the current one (1906), provided all the music. This organ was built by the Estey Organ Company of Brattleboro, Vermont and was a two manual and pedal organ of 10 ranks.
For the current organ that was installed in 1947, the majority of the pipes from the original organ of 1914 were rebuilt and installed in this organ. This organ was built and installed by the Wicks Organ Company of Highland Illinois. This organ is a three manual and pedal, of 29 ranks and 8 extensions, for a total of 2.059 pipes and Harp of 49 bars playable on the Great and Choir, and Chimes of 25 bells, also playable on the Great and Choir. This organ is completely enclosed in 3 chambers and the volume of tone from each pipe is under the complete control of the organist. Mr. Alfred Kuschwa of St. Steven's Episcopal Cathedral in Harrisburg Pennsylvania gave assistance with the specifications, voicing and final approval of this beautiful instrument.