Had all the bishops in the half century that followed the death of Bishop Elphinstone in 1514, been men of his same caliber, the Church of Scotland would have been in less urgent need of reformation than it was, and the reforming movement that eventually took place would have been less of a thorough-going character.
As it was, religious, social and political pressures combined to bring the movement to a head in 1560, with the abolition of Papal jurisdiction in Scotland and the repudiation of the mediaeval doctrine and practice of Mass, together with the adoption of a Reformed Confession of Faith.
Many of the artefacts associated with mediaeval worship became redundant and were cleared from the church over the succeeding generation. Rich church interiors were to be stripped and whitewashed, and iconography removed so that people would not be distracted from God’s glory.
The organ had already ceased to be used for worship in line with the new practices and in 1574 the civil authorities ordered that it be broken up and sold for the benefit of the poor. (Two hundred years later, pipework from this organ was found in St Mary’s Chapel!)
However, only about 10 percent of the population (mostly lairds, nobles and townsfolk) were actually Protestant at this time, so support for the widespread changes and destruction was limited, which may explain why some items have survived. Ill-informed anti-Calvinistic prejudice suggests that such post-Reformation worship spaces were bleak and bare. But evidence survives, both documentary and tangible (especially in carved wooden panels), of which many are now in St Mary’s Chapel), of careful craftsmanship devoted to the Kirk. The climax of these arts came in the 17th century and is exemplified in the set of four, large needlework panels,which are some of the Kirk’s greatest treasures.
In 1596, the wooden screen, which had separated the choir (for the clergy) from the nave (for the people), was replaced by a stone wall to produce two spaces in which preachers could be hears simultaneously. The nave became the Auld or West Kirk, while the choir was the New or East Kirk; the original crossing and aisles became mutual ground.
A notable figure from this time was one of the former commemorates, Dr William Guild (minister from 1631-40), who purchased the former Trinitarian Friary for the Incorporated Trades in 1633. The body, in turn, continues to be a benefactor of the Kirk and of which the Convener Court is “kirked” at St Nicholas’ each year in November.