The earliest, very enigmatic mentions concerning the organs in St. Anne’s Church date back to 1650, when a new instrument—most probably by Georg Nitrowski, most likely in the form of a positive—was installed on the organ loft erected between 1635 and 1645. This instrument was repaired in 1685 by Johann Barenstrop and in 1699 by Tobias Lehmann, who at that time were also working on the great organs in the Holy Trinity Church.

In 1710, Andreas Hildebrandt received this positive as part of the settlement for building a new instrument, or, as Paul Schmidt claims, the positive was sold to an unknown church.

Hildebrandt’s organ was the first and prototype instrument independently built by the Gdańsk organ builder. The architecture of the organ case, which is embedded into the balustrade of the organ loft, was replicated—though in different proportions—in many of his later instruments, including the preserved organs in Pasłęk. The design features outer pipe towers, lower and based on a triangular plan topped with crowns, separated from the central pipe tower—based on a hexagon and also crowned—by double pipe fields. The bellows were located in a closed chamber beneath the organ loft on the north side. Despite overpainting and minor losses of pipes, the prospect has survived intact to the present day. The specification of the instrument is preserved in a collection compiled by Johann Ephraim Eggert, a Gdańsk organist and carillonneur, in 1802.

The keyboard was placed at the back of the instrument, and the organist could see the liturgical action at the altar through an opening in the console cabinet and a longitudinal opening in the painting above King David’s head (now sealed).

In 1888, organ builder Julius Witt rebuilt the instrument, changing the position of the console and adding a two-stop pedal section.

Between 1910 and 1912, this instrument, together with its organ case, was completely rebuilt and replaced with a new pneumatic instrument (11/II/Ped) by Gdańsk organ builder Otto Heinrichsdorff. He installed his new instrument behind the Baroque prospect, which had been separated from the rest of the mechanism, probably incorporating some of Witt’s 1888 pipe material. During the Second World War, between 30 March and 19 April 1944, the organ case and its tin pipes were dismantled, transported, and stored in a parish barn in Lasowice Wielkie. After the war, the elements of the prospect were returned to the church, but were not immediately reconstructed. In 1945, the instrument was brought back into use by Friedrich Schwarz. Initially, the historical prospect was replaced by a modern, screen-type prospect composed of free-standing pipes from the great organ. However, during the renovation and reconstruction of the organ loft, the original 1710 prospect was also reinstated. In the absence of precise documentation, it may be assumed that this took place around 1968, simultaneously with the reconstruction of the 1703 organ balcony in the Holy Trinity Church. At that time the organ was supplemented by Józef Adamczyk and Ryszard Plenikowski from Kartuzy, using pipe material from the prospect pipes of the great organ from the Holy Trinity Church. Since then, the instrument was repaired only sporadically, merely to maintain minimal functionality. These unplanned and mutually incompatible repairs, however, led the instrument into increasing decay. A significant factor was also the severe infestation of the wooden parts by wood-boring insects, and the fact that the blower and bellows were placed in the church attic, supplying air with entirely different hydrothermal parameters than the atmosphere surrounding the pipework, which caused detuning and gradual degradation of the entire instrument. In recent years (2018–2019), partial technical operability—consisting of restoring the sound of some stops through temporary substitute materials in the wind system—was achieved thanks to repair work carried out by Józef Mossakowski from Grudziądz, father of the local organist (2018–2020), Michał Mossakowski.

Between 2021 and 2023, the instrument was meticulously restored to its original state, employing original solutions which, as it turned out, were structurally imperfect and most likely functioned inadequately from the beginning. A decision was made to significantly improve the functionality of the action through subtle modifications within the organ console.

Disposition after the completion of works
(in the order of the windchests from the prospect toward the rear of the organ)