In 1845 tragedy struck – fire gutted Old Greyfriars and destroyed the furnishings of New Greyfriars. Even today, the sides of the windows in the eastern part of the church show traces of fire damage. The restoration took many years – following the fire, the original roof and arcades were removed and, a few years later, a new, single-span roof introduced. The windows were made into lancets and stained glass – the first in any Scottish parish church since the Reformation was introduced in 1857.

At the same time, a movement began towards reviving a less puritanical style of worship. Worship in the Church of Scotland was notoriously austere, with long prayers and sermons. Music for psalm-singing was limited to a few tunes, and the setting for worship nearly always lacked ornament of any kind.  Rev Robert Lee, the minister at the time of the fire, saw an opportunity to reform aspects of worship and church order.

He introduced the aforementioned coloured windows, together with a pipe organ, liturgical worship and hymn singing; and he invited people to stand to sing and kneel to pray. Had Lee not suffered a stroke and been badly injured falling from his horse in 1867, he would have been called to the bar of the General Assembly and put on trial as an innovator. He died the following year, but his changes rapidly became the norm, and worship in the Church of Scotland was transformed.

Much of the stained glass in the Kirk is mid-Victorian and was installed as a permanent memorial to people who, in their day, occupied prominent positions in the Church. The large East Window depicts the parables of the Prodigal Son, the Good Samaritan, the Pharisee and the Publican, and the Wise and Foolish Virgins.