After the fire of the church in 1762, Josef Streussel, a prominent organ builder from Králick, began to build a new organ here. and the construction of the new organ in the Cathedral of the Holy Spirit. The new organ in St Mary’s Church will be the first time  2. 12. 1766.

In 1857 the church was again hit by a great fire, but there is no record of the organ being destroyed. The instrument was repaired and rebuilt several times in the past (1869 by Franz Kunz from Josefov, 1922 by Bohumil Paštika, around 1930 by Karel Ryglevič from Hradec Králové). In 1999, the restoration of the organ was completed by Ivan Červenka from Jakubovice for CZK 600,000. The missing tin pipes were supplied by Jan Kubát from Kaňek. The restoration of the organ case was done by Václav Molenda from Kutná Hora for 80 000 CZK.  

The two-manual instrument with 22 registers is also remarkable for the fact that its organ case is created by a unique illusory painting on wooden panels. It is also one of the few surviving instruments of organ builder Josef Streussel.