Under Elizabeth and James I the power of the Anglican state Church was extended over Ireland. The Church of England obtained all that belonged to the Church of the Pale and was invested with the establishment belonging to the Celtic Church as well. An ancient feud existed between these two Irish Churches, and they were intensely hostile to each other. The Church of the Pale was affected by the Reformation, but the Celtic Church had become increasingly Roman Catholic.

Nearly the entire Celtic population of Ireland and the majority of the inhabitants of the Pale remained Roman Catholic, and the Anglican Church served as a political instrument for the English rulers in Dublin Castle.

During the reign of James I English law was pronounced the sole law of the land. No longer able to act independently, the Earl of Tyrone and Rory O'Donnell, 1st Earl of Tyrconnel, with some 100 other chieftains, fled in 1607 to Rome. After the so-called "Flight of the Earls", the land in six counties of northern Ulster was confiscated and became the basis for the subsequent Ulster Plantation. 

The last vestiges of the independence of the Irish parliament were destroyed by the creation of 40 boroughs out of small hamlets, a political manoeuvre that secured a permanent majority to the English Crown. 

The stern but vigorous rule of Sir Thomas Wentworth, 1st Earl of Strafford, viceroy of Charles I, produced order and prosperity in Ireland. By balancing the number of Roman Catholics and Protestants in Parliament and holding out to the former the promise of toleration, he succeeded in obtaining liberal funds for the king in his conflict with the English parliament. The native Irish, who had been dispossessed in Ulster and elsewhere, made use of the English situation to regain their possessions. 

Under the leadership of the Irish chieftain Rory O'More, a conspiracy was formed in 1641 to seize Dublin and expel the English. The Irish succeeded in driving the English settlers out of Ulster and committed many outrages. English writers have estimated that at least 30,000 were put to death by the Irish, but this number is thought to be exaggerated; the Scottish in Ulster were, as a rule, spared. The insurgents were soon joined by the Roman Catholic lords of the Pale, and together they chose a supreme council to govern Ireland. Charles I sent Edward Somerset, Earl of Glamorgan, to treat with them, and the earl went so far as to promise them the predominance of the Roman Catholic Church in Ireland as the reward for their assistance to Charles. 

In 1647 the alliance between the lords of the Pale, who desired nothing beyond toleration for their religion, and the native Irish, who hoped for the restoration of the ancient land system, came to an end. 

In 1648 the Irish statesman and soldier James Butler, 12th Earl of Ormonde, returned as the viceroy of Charles I and made an alliance with the Roman Catholic lords, thereby securing Ireland to the Royalist party.