The 1911 organ served the congregation well until 1965 when the mechanisms and general condition of the instrument demanded fairly substantial restoration.

The opportunity was taken to rebuild the organ and bring the tonal specification up to date with current ideas. It incorporated most of the 1911 pipework, revoiced and rescaled to bring it into line with modern practice. New stops were provided, together with electro-pneumatic action and a new draw-stop console which was sited at the near the east wall of the chancel. The contract was placed in the hands of Messrs. J. W. Walker of Ruislip, Middlesex who were already recognised for their work at York Minster, Glasgow Cathedral and later at Paisley Abbey. It was also decided at this time to reduce the number of manuals to three but to have two divisions played from the Choir keys – that of Choir and Positive. The specification of the Organ following this extensive rebuilding process was as follows:

The Organ of Dunfermline Abbey 1966
rebuilt by J.W. Walker & Sons Ltd, Ruislip, Middlesex

Pedal Organ	Great Organ
32 Double Open Diapason 16 Open Diapason (ext) 16 Violone 16 Bourdon 16 Lieblich Bourdon 8 Violoncello 8 Bass Flute 8 Lieblich Gedeckt 51/3 Octave Quint 4 Fifteenth 4 Octave Flute III Mixture 22.26.29 16 Ophicleide (Tuba) 8 Tuba 8 Posaune (Gt) 4 Clarion (Gt)i Great to Pedal ii Swell to Pedal iii Choir to Pedal iv Great & Pedal Pistons Coupled	16 Double Open Diapason 8 Open Diapason 8 Stopped Diapason 8 Viola 4 Principal 4 Waldflute 22/3 Twelfth 2 Fifteenth IV Mixture 19.22.26.29 8 Trumpet  v Swell to Great vi Choir to Great vii Octave Couplers Off viii Doubles Off
Swell Organ	Choir Organ
8 Open Diapason 8 Rohrflute 8 Salicional 8 Voix Celestes (tc) 4 Principal 4 Octave Flute 22/3 Nazard 2 Fifteenth 1 Twentysecond III Scharf 22.26.29 8 Oboexi Tremulant16 Contra Fagotto 8 Cornopean 4 Clarionx Swell Octave xi Swell Unison Off xii Swell Sub Octave	8 Hohlflute 8 Dulciana 4 Flauto Traverso 8 Orchestral Oboexiii Tremulant8 Tuba (unenclosed)
Positive Organ  (playable from Choir keys)	Accessories
8 Bourdon 4 Principal 2 Blockflute 13/5 Tierce 11/3 Larigot III Cymbel 29.33.36 8 Regal xiv Tremulant xv Choir Octave xvi Choir Unison Off xvii Choir Sub Octave xviii Swell to Choir	6 Thumb Pistons to Great Organ 6 Thumb Pistons to Swell Organ 6 Thumb Pistons to Choir/Positive Organs 1 Reversible Thumb Piston Great to Pedal 1 Reversible Thumb Piston Swell to Pedal 1 Reversible Thumb Piston Choir to Pedal 1 Reversible Thumb Piston Positive to Pedal 1 Reversible Thumb Piston Swell to Great 1 Reversible Thumb Piston Choir to Great 1 Reversible Thumb Piston Swell to Choir 1 Reversible Thumb Piston Choir Tuba 1 Reversible Thumb Piston Pedal Ophicleide 1 Reversible Thumb Piston Choir on Choir 1 Reversible Thumb Piston Positive on Choir 1 Reversible Thumb Piston Choir/Positive on Choir 1 Thumb Piston General Cancel 6 Toe Pistons to Pedal Organ 6 Toe Pistons to Swell Organ 1 Reversible Toe Piston Great to Pedal 1 Reversible Toe Piston Swell to Great 1 Reversible Toe Piston 16 Ophicleide 3 General Thumb Pistons to entire Organ 3 General Toe Pistons to entire Organ 1 Thumb Piston Setter Balanced Expression Pedal to Swell Balanced Expression Pedal to Choir Push Button Control to Blower/TR Units Signal Lights to Choir/Positive Control Pistons adjustable by switches Manuals CC to C 61 notes Pedals CCC to G 32 notes Detached Console Electro-Pneumatic Action