When the new church building was being planned in the early 1960s, the church engaged the services of the noted organ consultant Dr. William H. Barnes of Evanston, Illinois, to supervise the creation of an organ of the exceptional versatility and size required by the new sanctuary. The Dayan Memorial Organ from the old church was retained, but as a separate ?antiphonal? organ playable either from the main console or from its own console in the balcony. The two organs separately and together for years served for service and recital use, and from time to time additions were made to bring the instrument closer to the scope of its original proposed design.

The organ was named in honor of its principal donor, Merritt C. Speidel, whose munificence during the last year of his life made possible an instrument of this size. The Swain and Kates Organ Company of Oakland originally installed the pipework (of tin, lead and zinc, and of Honduras mahogany), windchests and console, which were made by the historic organ supply firm of Aug. Laukhuff GmbH & Co. of Weikersheim, Germany. After the instrument was installed in 1963, Dr. Barnes himself played the dedicatory recital.

Over the years many distinguished guest recitalists have played recitals on the instrument, among them E. Power Biggs, Pierre Cochereau, Maurice and Marie-Madeleine Duruflé, Virgil Fox (who insisted that a very large mirror be mounted above the original, unmovable console for his recitals, in order to show off his technique to the audience), Jean-Louis Gil, Robert Glasgow, Gerre and Judith Hancock, Rodney Hansen, Peter Hurford, Wilma Jensen, Susan Landale, George Markey, Herbert Nanney, Robert Noehren, Flor Peeters, Simon Preston, John Rose, Michael Schneider, Frederick Swann, John Walker, and Todd Wilson.

One of the first additions to the organ after its first installation was the Trompette en Chamade, or horizontal fanfare trumpet, mounted high above the gallery organ, the gift of Mr. and Mrs. Bonnar Cox. A replacement gallery console to control the Antiphonal Divisions was presented in 1971 in recognition of the work of Eileen Washington upon her retirement after twenty-two years as Director of Music. In 1977 the Antiphonal windchests, dating from 1923, were replaced because of normal deterioration. In 1979 a new chancel console was installed to control the resources of both organs. Under the direction of David Parsons, organist from 1987 to 2004, in 1989, several quiet stops, of period pipework, were added to the Antiphonal Swell division in an attempt to reintroduce the sounds of some of the stops discarded from the 1923 instrument. In 1991, several damaged sets of pipes in the Chancel Organ were replaced with sets made in Holland and France, in order to provide clear and stable sounds especially for choral accompaniment. An Organ Committee, chaired by Dr. James Angell, reported to the Board of Trustees in 1991 concerning the continuing problems facing the chancel instrument. Subsequently the Administrative Council authorized the formation of a Task Force for the Centennial Organ Project, which would endeavor a) to complete the instrument, using as a guide the original proposed grand scheme, b) to rationalize the original scheme with the latest in organ scholarship, and c) to correct the mechanical and acoustical problems which had faced the instrument for years.

By 1992 it was clear that the leather valves of the chancel Swell division windchests were failing the most rapidly of any in the instrument. Without immediate attention, the division would have become completely unplayable. Thanks to the generous gifts of several members of the church, and the volunteer efforts of those who gutted and reconstructed the Swell chamber in preparation for the repairs, an entirely new Swell windchest was installed in 1993 by the Balcom and Vaughan Pipe Organ Company of Seattle. By 1997 it was evident that the Choir/Bombarde windchest was quickly deteriorating, just as the Swell had, and it was clear that it was necessary to replace it as well. Work on the newly-named “Positif” division was finished in 2000, and its full complement of pipes was finally installed in 2002. Both new windchests are of “slider” construction, which, in addition to being compact and reliable, involve none of the fragile leather valves of the type which had caused so many problems in the original instrument. Damaged pipes were replaced and several new sets of pipes added to both the Swell and Positif divisions. Some pipes from the exterior divisions were centralized into the interior, allowing for more flexibility, especially in choral accompaniment. Exterior pipes were cleaned and adjusted for uniform speech, with excellent results. In time for Christmas 2002, a set of chimes was given in memory of Robert Waitte, to replace the J. J. Morris Memorial Chimes, discarded in 1963. In 2004, MIDI control circuitry was added to the instrument, allowing the console to control external electronic devices and for computer sequencer software to play back the organ itself.

The instrument is now one of the largest in the San Francisco Bay Area, boasting numerous sets of ethereal soft string stops, in addition to many piquant flute stops, and all the stops required for accompanying congregational and choral singing, and for playing the organ literature of all periods.