Mounting tension against the attempts by Charles I to make the prayer book compulsory in Scottish churches and to re-impose an episcopal system with bishops led to open rebellion in Scotland at the end of the 1630s and to a series of civil wars in the British Isles which lasted until 1651. The National Covenant condemning recent innovations in worship and demanding a church free from royal interference was launched in Edinburgh at the end of February 1638. At the end of November, the General Assembly of the Church of Scotland met in Glasgow Cathedral. It abolished episcopacy (bishops) in the Kirk and brought in other religious reforms which underwrote presbyterianism.
People in Glasgow were generally strong supporters of the Covenanting movement, raising 19,529 Scots pounds [about £1,627 sterling] for the cause in 1640. A leading figure in the town during the 1640s was George Porterfield. He was involved in national Covenanting politics in the early 1640s and he helped supply the Covenanting army sent to Ireland in 1642. With the help of mainly Highland and Irish troops under James Graham, Marquis of Montrose, the royalists fought back and Montrose defeated Covenanting armies in a whole series of victories during 1645. After his victory at Kilsyth on 15 August, his troops plundered Glasgow and forced it to surrender. There were plans to convene a Parliament in Glasgow in October, but, before then, Montrose had been defeated at Philiphaugh. Now the town council was dismissed by the Covenanting leadership, fined 40,000 pounds Scots [£3,333], and Porterfield was made Provost and Member of Parliament from 1645 until 1651.
The Covenanting government in Scotland disapproved of the execution of Charles I in 1649 and proclaimed his son king, as Charles II. Conflict with Oliver Cromwell and the English Parliamentarians soon followed. Cromwell came to Glasgow in October 1650 after his victory at the battle of Dunbar. He stayed in lodgings in the Saltmarket at the house of Colin Campbell, a merchant and politician. He attended a church service in the Barony Church and was subjected to a sermon by Zachary Boyd, the Covenanting minister. One of Cromwell's officers described Boyd as an "insolent rascal" and sought permission to haul him from the pulpit. Tradition holds that Cromwell invited Boyd to dinner and then kept him on his knees in prayer for over three hours!
After the Restoration of Charles II in 1660, bishops and the selection of ministers by patrons rather than by congregations were again imposed. Ministers who would not accept this were ousted and often took large sections of their congregations with them. These would often be forced to meet in the open air in conventicles. Conventicles were being reported in Glasgow in the late 1670s. In October 1678 Archbishop Alexander Burnet (who was eventually assassinated) was attacked by a conventicle, including "great multitudes of women", which had been meeting in the Saltmarket. In 1679, after the victory of Covenanters at Drumclog, troops entered Glasgow, but were repelled by government forces in the streets around Glasgow Cross. The suppression of Covenanters continued in the early 1680s, during what were known as the "killing times", with various executions in Glasgow in 1684, including five at Glasgow Cross on 19 March.