A strip of land next to the Flodden Wall was purchased by the Town Council in 1703 and added to the kirkyard. A gate was built the following year. The area became known as the Covenanters’ Prison.
When the Lord Advocate, Sir George McKenzie of Rosehaugh who prosecuted the Covenanters died in 1691 he was buried in Greyfriars kirkyard. His tomb stands on the south side of the kirkyard close to the Inner Yard where the men, women and children captured at the Battle of Bothwell Bridge were held under armed guard.
In November the 257 prisoners who remained in the yard were marched to the Port of Leith and put on a ship bound for Virginia where they were to be sold as slaves. The ship ran into a storm off the Orkneys. The crew and forty eight prisoners managed to get ashore before the ship sank.
The men, women and children numbering over a thousand who had been captured during the battle were kept under armed guard in the Inner Yard of the burial ground without shelter. The wounded were sent to Heriot’s for medical treatment.
The Covenanters were defeated at the Battle of Bothwell Bridge which spans the River Clyde in June 1679 by the government army commanded by the Duke of Monmouth. Over one thousand men, women and children captured during the battle were marched back to Edinburgh.
The Bow Well at the foot of the West Bow was built in 1674. It was one of the twelve public wells to be set up in the town. The water came via a wooden pipeline from the Comiston Springs which lie the south of the city to the reservoir on the Castle Hill.
In 1659 a boarding school for boys without fathers was set up in Heriot’s Hospital. Although there was a chapel in the building the pupils also attended the services in Greyfriars where a section was set aside to accommodate them.
The church was converted into a barracks when Oliver Cromwell’s troops occupied Edinburgh in 1650. Heriot’s was also used to accommodate soldiers who had been wounded at the Battle of Dunbar. The church was used as a military barracks for three years. In addition to ransacking the church, the soldiers destroyed the pews and fittings.
The Reverend Robert Traill was appointed minister of Greyfriars in 1649. Born in Denino in 1603 he studied at St Andrews University. He was chaplain to the Scots Army at the Battle of Marston Moor.
The Reverend George Gillespie was minister of Greyfriars from 1642 to 1647. Born in 1613 he studied at St Andrews University.