The stained glass windows in Gordon Chapel were designed by Edward Burne-Jones and made by William Morris & Co. They are world-famous and the chief delight of Gordon Chapel. Like all of the churches in Fochabers, Gordon Chapel is on a NNE/SSW axis but, for simplicity in description, reference is made here to Ecclesiastical East  (i.e. behind the altar), West, North and South. The Lancet and Rose windows are on the East wall.

The Burne-Jones windows, made by William Morris & Company, were not part of the original design of the chapel but were added between the years 1874 and 1919.  Each of the windows commemorates a member or members of the Gordon Lennox family.  Although Edward Burne-Jones died in 1898, his drawings were used until the firm closed in 1940.  The tree-work backgrounds are particularly beautiful and elaborate and worthy of note.  The modern St Andrew window was added in 1990 to commemorate Sir George Gordon Lennox.

What was here before their installation is not entirely clear.  However, a clue is offered by two small coloured glass panels inset into the windows of the stairway leading to the chapel itself.  One depicts the arms of the Marquess Cornwallis and the other depicts the arms of the Duke of Bedford.  These noblemen were the brothers-in-law of George, 5th and last Duke of Gordon, the builder of the chapel.  It may well have been that these two windows, together with another three windows depicting the arms of the Duke of Richmond, Mr Charles Palmer and the Duke of Manchester (his other brothers-in-law) and subsequently lost, were inset into the original chapel windows and moved to their present location after the renovations of the 1870s.   Petri Anderson, the designer of the new Baxter window, has indicated however that these armorial windows are earlier in date and may have been inset into windows at the Castle originally.

During 2010 and 2011, the windows were removed during the construction of the Fochabers bypass.  They were conserved and restored by the Scottish Glass Studio in Glasgow and returned to the chapel in May 2012.  They have been restored to their original glory and were formally rededicated on Sunday, 12 August 2012.