Regrettably, an organ was not present at the grand opening of The Concertgebouw on 11 April 1888, even though there was space reserved for one. After a benefit concert and a lottery were held, an order was placed in 1890 with the Utrecht organ builder Michael Maarschalkerweerd, for the now-celebrated Concertgebouw organ, for a price of 22,352.89 guilders. The organ case would be made by Dolf van Gendt.
In October 1990, the organ company Flentrop Orgelbouw kicked off a complicated two and a half-year restoration process that started with the disassembly of the organ. The inaugural concert for the restored organ on 18 March 1993 demonstrated that the intended goal had been achieved: the organ had regained its original tone, and the mechanics had been updated for modern use. The organ had been granted a second lease on life.