In 1637, Charles attempted to impose a new prayer book on the Kirk, laying down forms of worship in line with those favoured by the High Anglican Church. The reformers denounced these changes as 'popery' and organized the National Covenant, a religious pledge that committed the signatories to 'labour by all means lawful to recover the purity and liberty of the Gospel as it was established and professed'.

Charles declared all the 'Covenanters' to be rebels, a proclamation endorsed by his Scottish bishops. Consequently, when the king backed down from military action and called a General Assembly of the Kirk, the assembly promptly abolished the Episcopacy. Charles pronounced the proceedings illegal, but lack of finance stopped him from mounting an effective military campaign - whereas the Covenanters, well-financed by the Kirk, assembled a proficient army under Alexander Leslie. In desperation, Charles summoned the English Parliament, the first for eleven years, hoping it would pay for an army. But, like the calling of the General Assembly, the decision was a disaster and parliament was much keener to criticize his policies than to raise taxes. In response Charles declared war on parliament in 1642.

Until 1650, Scotland was ruled by the Covenanters, and the power of the Presbyterian Kirk grew considerably. Laws were passed establishing schools in every parish and, less usefully, banning trade with Catholic countries. The only effective opposition to the theocratic state came from the Marquis of Montrose, who had initially supported the Covenant but lined up with the king when war broke out. His army was drawn from the Highlands and Islands, where the Kirk's influence was weakest. Montrose was a gifted campaigner who won several notable victories against the Covenanters, but the reluctance of his troops to stay south of the Highland Line made it impossible for him to capitalize on his successes, and he was eventually captured and executed in 1650.

Largely confined to the peripheries of Scotland, Montrose's campaigns were a side-show to the Civil War being waged further south. Here, the Covenanters and the English Parliamentarians faced the same royal enemy and in 1643 formed an alliance. Indeed, it was the Scots army that captured Charles at Newark in Nottinghamshire, in 1646. There was, however, friction between the allies. Many of the Parliamentarians, including Cromwell, were Independents, who favoured a looser form of doctrinal control within the state Church than did the Presbyterians, and were inclined towards religious toleration for the law-abiding sects outside the state Church. In addition, the Scots believed the English were tainted with Erastianism - a belief in placing the secular authority of Parliament over the spiritual authority of the Church.

The Parliamentarians in turn suspected the Scots of hankering for the return of the monarchy, a suspicion confirmed when, at the invitation of the Earl of Argyll, the future Charles II came back to Scotland in 1650. To regain his Scottish kingdom, Charles was obliged to renounce his father and sign the Covenant, two bitter pills taken to impress the population. In the event, the 'Presbyterian restoration' was short-lived. Cromwell invaded, defeated the Scots at Dunbar and forced Charles into exile. Until the Restoration of 1660, Scotland was united with England and governed by seven commissioners.

Although the restoration of Charles II brought bishops back to the Kirk, they were integrated into an essentially Presbyterian structure of Kirk sessions and presbyteries, and the General Assembly, which had been abolished by Cromwell, was not re-established. Over 300 clergymen, a third of the Scottish ministry, refused to accept the reinstatement of the bishops and were edged out of the Church, forced to hold open-air services, called Conventicles, which Charles did his best to suppress. Religious opposition inspired military resistance and the Lowlands witnessed scenes of brutal repression as the king's forces struggled to keep control in what was known as 'The Killing Time'. In the southwest, a particular stronghold of the Covenanters, the government imported Highlanders, the so-called 'Highland Host', to root out the opposition, which they did with great barbarity.

Charles II was succeeded by his brother James VII (James II of England), whose ardent Catholicism caused a Protestant backlash in England. In 1689, he was forced into exile in France and the throne passed to Mary, his Protestant daughter, and her Dutch husband, William of Orange. In Scotland, William and Mary restored the full Presbyterian structure and abolished bishops, though they chose not to restore the political and legal functions of the Kirk, which remained subject to parliamentary control. This settlement ended Scotland's religious wars and completed its reformation.