It can be reasonably assumed that most of the settlers who came to Ulster in the early seventeenth century were Protestants, even if only nominally so. The Church of Ireland was the established or state church and was organised along episcopalian lines with a hierarchy of clergy. However, several ministers from Scotland came to Ulster in this period who dissented from this view of church government, preferring the more egalitarian presbyterian system. To begin with, such men were tolerated within the Church of Ireland and there was no distinct Presbyterian denomination at this time.
In the 1630s the government began to clamp down on the activities of ministers with Presbyterian convictions. Those ministers who were not prepared to renounce their Presbyterianism were excommunicated.

In 1636 some of these men, with about 140 followers, set sail in the Eagle Wing for America; they never reached their destination, as storms drove the ship back. Many other Presbyterians returned to Scotland. Here Presbyterian opposition to Charles I was also reaching boiling point. In 1638 the National Covenant was drawn up in Scotland which declared Presbyterianism the only true form of church government and bound the nation to the principles of the Reformation. Many in Ulster also signed the Covenant. In response Wentworth insisted that all Scots in Ulster over the age of 16 take an oath – the infamous ‘Black Oath’ as it became known – abjuring the Covenant. Those who refused to take the oath could be fined and imprisoned. The result was that large numbers of Scottish settlers fled to their homeland; so many left, in fact, that in some places there were not enough people to bring in the harvest.

Catholic settlers were not entirely unknown in early seventeenth-century Ulster. There was a small, but significant, colony of Scottish Catholics at Strabane, under the patronage of Sir George Hamilton of Greenlaw, whose father was Lord Paisley, a prominent supporter of Mary, Queen of Scots. As early as 1614 Sir George’s Catholic sympathies were a source of concern for the government, and in 1622 he was described as an ‘Archpapist and a great patron of them’; it was noted that all his servants were Catholics. In the late 1620s the Church of Ireland Bishop of Derry became particularly agitated at the large number of Scottish Catholics he believed were living at Strabane under the patronage of Sir George Hamilton and his near relations.

The numbers killed in the rebellion have been a source of contention ever since the autumn of 1641. At the time, wildly exaggerated estimates – often considerably more than the entire British population in Ulster at the time – were circulated, mainly in the English press to drum up support for crushing the rebellion. Nonetheless, thousands of settlers did die in the rebellion, at least as many from exposure and disease as from murder. Those who had the means of doing so fled to Dublin or across the Irish Sea to England and Scotland. Others sought refuge with the towns that had not been captured.

In north-west Ulster resistance to the rebels was organised by the Stewart brothers, Sir William and Sir Robert, who recruited an army from among the settlers known as the Laganeers, one of the most efficient fighting machines of the war. Additional support for the settlers came in the form of a Scottish army, under the command of Major-General Robert Munro, which landed at Carrickfergus in April 1642. The conflict continued for the rest of the 1640s, and it was not until Cromwell arrived in Ireland in August 1649 that the island began to be brought under control. In Ulster most of the Scots supported the claims of Prince Charles, son of the recently beheaded king. Derry was briefly besieged by the Scots and in December 1649 an army of Scottish settlers was decisively defeated by a Cromwellian force at Lisburn.

By the second half of the seventeenth century the Presbyterian Church had emerged as a distinct denomination and there were clear lines of demarcation between it and the Church of Ireland. On the whole Scottish settlers were Presbyterian, while English settlers were Anglican, although there were numerous exceptions to this rule. In County Antrim Presbyterians formed an absolute majority. In 1673 Plunkett commented that in the dioceses of Connor and Down (comprising almost all of County Antrim and north and east County Down), the Presbyterians – ‘whose belief is an aborted form of Protestantism’ – were more numerous than Catholics and Anglicans put together. On another occasion he wrote that ‘one could travel twenty-five miles in my area without finding half a dozen Catholic or Protestant families, but all Presbyterians’. In 1683 Richard Dobbs noted that all the inhabitants of Island Magee in County Antrim were Scottish Presbyterians.

In the early eighteenth century there occurred the first major dispute within Irish Presbyterianism. This was over the issue of subscription to the Westminster Confession of Faith. Those who denied the necessity of subscribing to the Confession were known as New Light Presbyterians. In 1725 for the sake of convenience those who took this stance were placed in the Presbytery of Antrim. Other brands of Presbyterianism originating in Scotland were established in Ulster during the course of the eighteenth century. The Seceders, as they were known because they had seceded from the Church of Scotland in 1733, soon established congregations and presbyteries in Ulster. The first Irish presbytery of the Reformed Presbyterian Church was established. The origins of this denomination went back to the National Covenant of 1638 and the Solemn League and Covenant of 1643. The Reformed Presbyterians, or Covenanters as they were also known, refused to accept that the state had any authority over the church and did not participate in parliamentary elections. Both of these denominations provided an alternative to mainstream Presbyterianism.