In 1894, St. John’s first organ was built and installed in the sanctuary, then located at 12th and K Streets, by Felix F. Schoenstein of San Francisco, utilizing his tubular pneumatic system.

On October 6, 1912, a newly built sanctuary at 17th and L Streets was dedicated. Included in the new worship space was a Murray Harris pipe organ with 18 ranks of about 1,100 pipes. It was beautifully voiced by a local theatre organ company.

In 1967, St. John’s celebrated its 100th anniversary. Under the direction of Senior Pastor Robert Romeis, the sanctuary was extensively remodeled, complete with a new, much larger pipe organ designed by Swain and Kates, Inc. of San Francisco. Opus 52 had a four manual keyboard, 70 ranks, and 3,577 pipes arranged in 6 divisions: The Great, Pedal, Positive, Swell, Choir, and Antiphonal.

Then in 2007, anticipating the needs of St. John’s in the 21st century, a restoration of the sanctuary and adjoining spaces was undertaken. Many issues were addressed in the planning stages, including the fitness of the existing organ, as well as the inadequate acoustics in the sanctuary space. Ultimately, a new instrument was commissioned by the congregation .