Built at the same time as the organs for Exeter and Hereford Cathedrals, the St Machar's organ then consisted of two manuals and pedals with provision for a substantial unenclosed Choir department, a Pedal Ophicleide and a Swell Vox Humana, all of which were added by Willis in 1898. The action was Willis' patent tubular-pneumatic. In its original form the organ served well until 1928 when, having deteriorated badly, and with the building's interior about to undergo extensive restoration, it was taken down and completely rebuilt by Messrs Rushworth & Dreaper of Liverpool. 

On completion of the building’s restoration the organ was re-erected in its present location in the North aisle, in more or less the siting that had originally been envisaged for it. A modern drawstop console and an excellent new supply pneumatic action were fitted. The Choir division, in accordance with contemporary fashion, was placed ‘under expression’ (the pipes being placed in a separate compartment fitted with shutters, which could be opened and closed by means of a mechanism from the console in order to vary the volume) and the Swell Bourdon was transferred there, also appearing on the Pedal at 16ft and 8ft as the organ's first really soft bass stop. Its place on the Swell was taken by a double reed. In this form, the organ remained until 1956 when, in the course of cleaning and overhauling by Rushworth & Dreaper, the Swell Vox Humana gave place to a 3 rank Mixture and the Pedal received the addition of Open Wood extensions at 8ft and 4ft (since removed).

By the end of the 1960s the organ was once again becoming mechanically unreliable and, in 1973, its second major rebuilding was undertaken by the London firm of Noël P. Mander. A new console was provided, retaining and refurbishing the original Willis keyboards. The pneumatic actions gave place to electrics, the Swell received a Clarion and new upperwork, the Pedal division was made more suitable for present day requirements, and the Choir, once again made unenclosed, was partially remodelled. Further additions to the organ remain provided for.

In 1991, following cleaning work on the building's interior, the organ was cleaned and overhauled once again. This work was carried out by A. F. Edmonstone of Perth in whose care the organ had been for many years and who had renewed all stop switches and fitted a solid-state piston system in 2001. “

In the summer of 2018 when the cathedral was closed for some building works, three ranks of Willis pipes dating from 1898, which were stored in the organ (Dulciana 8, Claribel Flute 8, and Concert Flute 4), and which had been replaced by three Mander ranks in 1973 (Principal 4, Fifteenth 2, and Cymbale (26 29 22)), were reinstated by Harrison & Harrison of Durham, in whose care the organ currently stands. This has restored the character and variety of the Choir organ as envisaged by 'Father' Willis. The Mander pipes, which were removed to make way for the reinstatement, are now stored in the organ case. 

Work to improve the organ, in memory of, and as a tribute to, the generosity of James Lobban, Organist of St Machar’s Cathedral (1981-2006) and Musical Director of the Aberdeen Bach Choir (1969-2006), was suggested by Peter Parfitt, supported by the Aberdeen Bach Choir committee on behalf of the choir, supervised by Roger Williams and funded jointly by the Bach Choir and St Machar’s Cathedral. This concert is planned and presented deliberately to feature the Willis organ in all its glory, and to draw attention to this work.