After the 1709 fire had destroyed almost all of the church equipment, a need for a new pipe organ arose. The provisional instrument, from 1716, built by Antonín Schack, has stayed in the church up to these days.

The construction itself began in 1730 under Josef Emanuel Heintzler, a pipe organ builder from Olomouc, who died shortly after the construction start. Kryštof Zikmund Klembt from Kroměříž was entrusted with the continuation of the work – unfortunately, he met a similar destiny as his predecessor.

In 1740, Michael Engler, a well-renowned pipe organ builder from Wroclaw (Silesia), was named the head of the construction. The organ cabinet decoration was created by Olomouc sculptors Filip Sattler and Jan Antonín Richter. With its 3 manuals, 44 ranks and ca 2500 pipes, the finished instrument was the largest pipe organ in Moravia at the time. For both its size and beautiful sound, the instrument was called as The Queen of Moravian pipe organs. The whole construction cost was close to 19 000 gulden.

The pipe organ was played on for the very first time on 21th of September, 1745, a night before the feast of St. Maurice. With that, the instrument was passed for usage.

In the upcoming years, the technical conditions of the pipe organ worsened. The instrument underwent a reconstruction in the 19th century, however, it became nearly unplayable during the 20th century.

Because of the poor conditions of the pipe organ, another reconstruction, managed by Rieger-Kloss from Krnov, took place in 1959-1971. To prevent the original Engler work, the instrument was widely extended and a new organ console was installed, creating the largest pipe organ in the Czechoslovakia. The cost of the renovation was around 3 million Czechoslovak crowns. This renovation and modernization opened new musical possibilities of the classical Baroque instrument. As of today, the pipe organ has 5 manuals, 95 ranks and 8012 pipes.