The Great Court Organ has been rebuilt between 1858 and 1862 by the German-Swiss organ builder Friedrich Haas (1811–1886). The baroque instrument was transformed into a romantic concert instrument, among other things by expanding it from 48 to 70 stops and from two to four manuals with pedals. The attic also housed the Fernwerk, which is still preserved today and was financed by Haas himself due to his daring nature. It featured the world’s first known rain machine, which has been astonishing audiences ever since with “organ thunderstorms.” After completion of the work, the experts at the time concluded in their report that the organ “can be described and declared a masterpiece.” And there was something else that could have been an attraction: the organ, built between 1640 and 1648 by Johann Geißler of Salzburg († ca. 1670), contains the largest organ pipe in Switzerland, measuring 572 mm in diameter and 10.7 meters in length, which was even the largest in the world at the time. The magnificent main case, created at the same time by Niklaus Geisler (1585–1665) from Lucerne, still adorns the instrument today.

Even after the changes made around 1860, the Great Court Organ was not only tuned, regulated, and repaired time and again, but also underwent major renovations. This was the case in 1898/99, for example, when Haas was succeeded by Friedrich Goll (1839–1911). The maintenance carried out since 1972 by the Kuhn organ building company in Männedorf can be considered a major turning point in the history of the instrument. In 1977, 2001, and 2015, the instrument was gradually redesigned using the old pipes (around 70 percent) from Geißler, Haas, and Goll in combination with new pipes. After the first restoration by Kuhn in 1977, a part of the pipework that was no longer in use was stored in the church attic. Some of these pipes, which were originally part of the main organ, were incorporated into the new echo section built by Kuhn, which was completed in 2015. Some other pipes are still stored in the attic.
In addition to the main organ in the gallery, the impressive instrument now also features a Rückpositiv, a Fernwerk, and the new echo organ. It is this synthesis of different architectural styles and eras from the 17th to the 21st century that makes the Great Court Organ so unique. With 103 stops and approximately 7,500 pipes, it is one of the largest organs in Switzerland.