The organ in the Chapel was originally built in 1879 by Hilborne Roosevelt of New York City and installed in the chancel choir gallery of St. Stephen's Roman Catholic Church on East 28th Street. Roosevelt's Op. 53 had mechanical action controlling one five stops on one manual. In 1920, St. Stephen's commissioned W.W. Kimball of Chicago to build a new four-manual organ (K.P.O. 6567). Kimball retained and electrified the Roosevelt organ as the Chancel division of the new instrument.
In 2012, J.H. & C.S. Odell of East Haddam, Conn., was contracted to restore the Roosevelt organ to mechanical action and install it in the new Chapel of the Sacred Hearts of Jesus and Mary. Odell reused the original double-rise reservoir but built an entirely new chassis. A new case of quarter-sawn white oak with ebony accents has a façade which includes ten new speaking pipes of the 8' Open Diapason. The organ's pitch is A=455, and the wind pressure is 64mm (2½ inches).