Repairs and alterations
Alexander Henderson's successor was Patrick Scougal, under whose leadership substantial repairs and a number of alterations were carried out, which completely, changed the original layout of the church and enabled the growing congregation - it was the largest parish in Fife at the time - to be accommodated.
- The nave was extended to the west and given a lower roof line
- The dilapidated bell tower was rebuilt
- A carved rood screen was removed from across the chancel, by order of the General Assembly which considered its carvings to be idolatrous
- The chancel was closed off by a heavy partition with a small single door, and two mullioned windows were inserted in the chancel wall to provide light
- Galleries were built under the low plastered ceiling
- A two-tier pulpit was placed on the south wall (where the south entrance is now)
- The Leuchars aisle, for the use of Castle residents, was built out to the north
Scougal left Leuchars to become the Bishop of Aberdeen. There is a large stone dedicated to him by the north chancel wall. Dated 1674, is the oldest gravestone to have been found in the graveyard (others are no doubt older but their dates are illegible).
In the early part of the 18th century, during the Jacobite rebellion, the services were seriously disrupted and both the church and the castle began to crumble. In 1745, a major preoccupation of the minister and his Kirk Session was once again the business of restoring St Athernase, as follows:
- The roof and south wall were repaired
- The bell tower was rebuilt, using the octagonal design which remains a distinctive feature in the 21st century
The chancel was the venue for meetings of the Kirk Session, and a metal door was added to the existing stone cupboard to provide a safe place for offerings to be stored between services.
Both chancel and apse were used as storage space for Communion tables and, in times of meagre harvests, foodstuffs to relieve the plight of the poor.
In 1843 the Disruption gave birth to the Free Church and, like many congregations throughout the country, St Athernase was not left unscathed as people left the parish churches to join the new congregations.
Records say that the then minister of St Athernase, David Watson, was left with a small congregation, only two elders and a dilapidated church. This had major financial implications and in 1857, John Milne of St Andrews was asked to modernise St Athernase as cheaply as possible:
- The nave was pulled down and extended to the north
- The ceiling was heightened
- A gallery was added to the inside of the nave
- The chancel and apse were restored and excavated to their original depth
- Two windows in the south wall of the chancel were removed
- Exterior stonework on the Norman part of the building was restored
Further alterations were instigated in the early years of the 20th century:
- A wooden screen was placed between the apse and chancel, blocking off the original Norman church
- The floor of the nave was lowered by 25 inches to reveal the foot of the chancel arch
- The pews, Communion table, pulpit and Dutch reproduction chandeliers (given by Mr R.W.R. Mackenzie, owner of Earlshall) were put in place and are still in use today
The Rev. Dr William Levack, minister between 1907 and 1923, proposed that the apse and chancel should be opened up and brought into use once more. He removed the wooden screen and transferred it to the main vestibule, where it has remained. A Chaplain in Malta during the First World War, Dr Levack is commemorated in the only stained glass window in the church. By the renowned artist William Wilson, it depicts a biblical scene from John's gospel.