Cromwell died in 1658. One of his generals marched on London, dissolved Parliament and put the son of Charles I, Charles II, on the throne. When Charles II returned from exile in 1660, he endorsed the restoration of episcopacy and the use of the Episcopalian Common Book of Prayer. By order of King Charles II, the corpse of Cromwell was disinterred from its burial site at Westminster Abbey, hanged, and beheaded in 1661. Charles II considered Presbyterianism "not a religion for gentlemen."

On May 17, 1661, Parliament passed a resolution that the Presbyterian Covenant should be publicly burned. On May 30, 1661, a Bill declared the Solemn League and Covenant illegal. In 1662 an Act of Proclamation banned all ministers who did not have an Episcopalian Bishop’s license. All ministers chosen since 1749 were required to resign and reapply for their posts from bishops and lairds, the local parishes no longer having the power to designate their clergy. One third of the Scot ministers refused and held service in defiance of the law. The term "Covenanter" arose.

A small group of Covenanters murdered Archbishop Sharp in 1769. Troops were sent to enforce the law and quartered in the homes of recusants. This period was known as the "killing times." Over three hundred ministers were ejected from their manses. There were further bloody battles and over 100 prisoners taken and executed after various degrees of torture.

In the Act of Uniformity, Parliament began a program of prosecution of Puritans (and later in 1673 was to pass the Test Act, which barred all but Anglicans from public office). The core of the policy of revenge against Protestants was codified in the so-called Clarendon Code, four acts of Parliament passed between 1661 and 1665.

In 1672 an Act was passed punishing preachers at conventicles with death and imposing fines, imprisonment and exile for having children baptized by deprived ministers and for absence for three Sundays from the parish church. By 1697, 17,000 had suffered fines or imprisonment for attending conventicles. A host of 10,000 men, chiefly Highlanders, was quartered in the western shires in order to force the landowners who favored the Covenanters to enter into bonds.

No Scot Parliament had been held since 1674. Shorlty before the murder of Shaprp, the head of the Privy Council, Lauderdale, was said to have hoped for a rebellion by the Scots. "Would to God they would rebel that he might bring over an army of Irish Pqpists to cut their throats."

In 1678, after after being tortured severely, a preacher, Mitchell, who years previously had slain the bishop of orkney, confessed to his crime, was tried and executed.

In 1679 a Covenanter army of over 5000 soldiers was decisively defeated at Bothwell brig by Monmouth with 400 left dead and over 1500 taken prisoner. The names of all Covenanter martyrs are recorded on the National Covenant Memorial in Greyfriars Kirkyard. Two ministers were hung and the others executed. Two women were made martyrs when they were tied to posts in the tidelands and left to drown in high tide. Some two hundred were sentenced to transportation to the West Indies but their ship sunk and they drowned, among them a Caldwell. Between 1660 and 1690 about 30,000 Presbyterians migrated to Ulster (Northern Ireland). Most of these entered Ulster through Londonderry.

The strongest and most extreme forms of covenanting and resistance were found in Ayrshire, Dumfries, and Galloway where dissenting ministers had large congregations. Their resistance took the form of guerilla tactics. They were subjected to heavy-handed military and judicial reprisals, especially after 1681. The estates of the defeated covenanters were forfeited. Among such forfeitures was the Mure of Caldwell Estate.