James VII and II had succeeded his brother Charles II in 1685, but his arbitrary government and fears that he would attempt to spread Roman Catholicism led to discontent in all parts of his Kingdom. Encouraged by powerful aristocrats in England, the King's son-in-law, William of Orange, invaded. James fled and William and his wife Mary took the throne in what became known as the "Glorious Revolution". Scotland followed the English lead and accepted William and Mary.
When the new Protestant monarchs were proclaimed in Glasgow, university students burned effigies of the Pope and of the Archbishops of Glasgow and St Andrews. Several Episcopalian ministers were "rabbled" out of their parishes and their families and property attacked. A service in the Cathedral was broken up.
The new provost was John Anderson of Dowhill and it was he who represented the burgh at the 1689 Parliament, strictly the Convention of Estates, which declared that James had forfeited the throne. Anderson was a supporter of the Williamite cause and he served on many of the leading committees of the Convention. Glasgow was an important strategic location for the new government in its continuing war in Ireland, to where James had fled. Anderson was responsible for moving ammunition from Stirling Castle to the Glasgow Tolbooth. Troops were quartered in the town, including Danish and English regiments en route to Ireland. Glasgow merchants were involved in chartering ships for transporting the troops. Many protestant refugees from Ireland fled to the west of Scotland and John Hall, one of the baillies, took an active role in collecting money for their relief. In 1690 bishops were once again removed from the Kirk and a Presbyterian structure restored.