The 1641 rebellion halted but did not stop the progress of the Plantation settlement and British (and particularly Scottish) migration to Ulster resumed after the war. In 1659, almost a third of the population in the province were of British origin; and by the mid-18th century Protestants were in the majority. By the late 17th century also, the population in Ulster was geographically divided with those of Irish extraction living on poor quality and marginal lands and the British community were settled on the better agricultural land. The Ulster Plantation, thus, determined the long term division of the province into Protestant and Catholic communities.
The tension and suspicion between the two groups initiated during the early years of the Plantation was intensified as a consequence of the wars of the 17th century. The massacres of 1641 left permanent and deep scars in the group memory of the Protestant settlers. The accession of the Catholic King James II to the English throne in 1685 revived fears that the landed wealth and political power of Irish Protestants would be undermined. The birth of a son to Jamesís wife in 1688 was the signal for Jamesís son-in-law, the Protestant William of Orange to invade England and claim the English throne in the name of his wife, Mary. Williamís actions received strong support among Irish Protestants. The subsequent war of the two kings, William III and James II on Irish soil in 1689 further exacerbated the hostility between Catholics and Protestants, particularly in Ulster where William III was subsequently identified as a defender of Irish Protestantism.
The wars of the 1640s also strengthened the position of the Presbyterian Church in Ireland. The first presbytery was established in Belfast in 1642 and from then on Presbyterianism began to develop its own institutional infrastructure. The earliest session records date from 1646 and testify to the strong sense of community encouraged by the church and also the strict moral code which church members were obliged to observe. In the 18th century Presbyterianism continued to be a major ideological force in Ulster and was reinforced through a popular evangelical movement. Allegiance to Presbyterianism was also strengthened by legislation designed to establish conformity to the Church of Ireland.
The penal legislation of the Irish parliament at the end of 17th and beginning of the 18th century discriminated against all dissenters from the established church although it was primarily directed at undermining Catholicism. Contrary to the intentions of the legislators, however, the laws had the effect of consolidating allegiance to Catholicism and Presbyterianism and intensifying the existing divisions in society.
Economically, the province benefited from the expansion of the linen industry in the late 17th century. Many of the second and third generation of settlers grew flax and spun and wove yarn in addition to tending a small farm. The perception of the Protestant settler as an enterprising and hardworking individual (although usually portrayed as a man) dates from the middle decades of the 18th century when linen exports soared and the rural economy prospered.