The Reformation, before which, in 1532, Henry VIII of England broke with papal influence, completely altered Ireland. Henry separated English Catholicism from Rome, and his successor Edward VI of England raised the bar even more by breaking with papal doctrine entirely. While the English, Welsh and Scots converted to Protestantism, the Irish remained Catholic, which determined their relationship with the British state for the next 400 years. The Reformation happened at the same time when the English wanted to colonise Ireland.

From 1536, Henry VIII wanted to re-conquer Ireland and take it under his crown. The Fitzgerald dynasty of Kildare, who had been the rulers of Ireland in the 15th Century, had grown into unreliable allies of the Tudor monarchs. They had invited Burgundian military parts into Dublin to crown the Yorkist pretender, Lambert Simnel, as King of England in 1497. Again in 1536, Silken Thomas Fitzgerald openly revolted against the crown. Having stopped this rebellion, Henry VIII decided to conquer Ireland politically, so that the island would not be a starting point for future rebellions or foreign invasions to England. In the mid-16th Century, Henry proclaimed Ireland from a lordship to a complete kingdom. Henry was officially acknowledged King of Ireland at a meeting of the Irish Parliament, the first meeting of parliament when Gaelic Irish chieftains, as well as the Hiberno-Norman aristocracy, were present. The expansion to control the English Kingdom of Ireland took nearly a century, with various English administrations either negotiating or fighting with the independent Irish and Old English lords.

The re-conquest of Ireland was conducted during the reigns of Elizabeth I and her heir James I, after the few bloody conflicts of the 1569–73 and 1579–83 Desmond Rebellions and the 1594–1603 Nine Years War. Afterwards, English authorities in Dublin gained real control over Ireland for the first time, bringing a centralised government to the entire island and successfully disarming the native lordships. However, the English did not have success in converting the Catholic Irish to the Protestant religion, and the brutal methods used by the crown to pacify the country heightened resentments of English rule.

From the mid-16th and into the early 17th Century, crown governments carried out a policy of colonisation known as “Plantations.” Scottish and English Protestants were sent as colonists to the provinces of Munster, Ulster and the counties of Laois and Offaly. These British-Protestant settlers would form the ruling class of future British administrations in Ireland. A series of Penal Laws were drawn up, which discriminated against all faiths, other than the established Anglican Church of Ireland.