The instrument was completed in 1686 by Roelof Barentsz and Johannes Duyschot. At that time it had two manuals and pedal. A Bovenwerk was added by Christian Vater in 1727. In the following centuries, the organ was altered many times in order to adapt it to continually fluctuating sound ideals. Following the restoration of 1939, an untenable situation had arisen in all respects.
In the period 1989–1992 the organ was rebuilt by Flentrop Orgelbouw using the situation of 1686/1727 as a point of departure. Only about 600 pipes from that period were still present in the instrument. 3,000 new pipes were made based on analysis of the material still present. Three reeds were added to the old disposition: Dulciaan 8', Fagot 16', and Trompet 4'. The original windchests, still present in altered form, were restored. Mechanical action was once more provided, new keyboards and stopknobs were constructed in the original style. The front pipes (1845) of the Hoofdwerk, Rugwerk and Pedaal were retained. The Baarpijp dating from 1895 was again introduced. The 17th century pitch, a'=460 Hz., was altered to a'=440 Hz. by means of moving up the pipework. Equal temperament was the chosen tuning. As a result, combination with other instruments and the performance of 19th and 20th century music was made possible.
The parts remaining from the old organ were too fragmentary to be able to speak of a restoration or reconstruction. Rebuild is the most suitable term. The original case, windchests, and about 20% of the pipework from the 17th and 18th centuries made their mark on this project. The creative interpretation of the past by the organbuilders certainly contributed to the result: an organ with historical roots that is also usable for the cultural and religious function of a large city church.
The inside of the organ shutters of the Hoofdwerk was painted by Gerard de Lairesse, on the left panel we see the dancing and playing King David in front of the Ark of the Covenant. On the right panel we see the Queen of Sheba presenting gifts to King Solomon. Both stories in the book of Kings in the old testament of the Bible. Gerard de Lairesse was born in Liège in French Belgium in 1640 and he moved to Amsterdam in 1664; in the second half of the 17th Century, he was one of the most popular painters in the Netherlands. At this moment, the shutters of the Duyschot organ can be seen on a retrospective of the work of Gerard de Lairesse at the National Museum Twente in Enschede, the outside paintings of these panels or shutters were lost in the 19th century when the church wanted to sell them. The grisailles on the Rugwerk panels were also painted by Gerard de Lairesse; The four evangelists with their items are showen. The inside of the Rugwerk shutters have paintings of old musical instruments, the complete organ was cleaned and re-painted in 1992 in its original state of colour in 1686; most of it in marble imitation.
The small organ was built in 1963 by D. A. Flentrop. The congregation presented it to the then minister of Westerkerk, Ds. H. A. Visser. The organ was restored in 1999–2000 by Flentrop Orgelbouw. At the rededication it was given the name Ds. H. A. Visser organ.