The  Rising in 1641 was followed by the formation of the Catholic Confederation which became the de facto government of Ireland, free from the control of the English administration and loosely aligned with the Royalist side in the Wars of the Three Kingdoms.

The subsequent Irish Confederate Wars continued in Ireland until the 1650s, when  Oliver Cromwell’s New Model Army decisively defeated the Irish Catholics and Royalists, and re-conquered Ireland.

Oliver Cromwell, a Puritan and Republican, believed he was an instrument of divine retribution for (alleged) atrocities committed by Catholics against Protestants in 1641 and he accordingly gave orders to deny mercy to Catholics. His campaign was savage and is remembered for the slaughter of women and children as well as unarmed captives. As a result of deaths from war, killings, plague, disease, exposure to the elements, famine, and deportations the population of Ireland fell by an estimated one third to a half.

Cromwell imposed an extremely harsh settlement on the Irish Catholic population. Many implicated in the rebellion of 1641 were executed. Those who participated in Confederate Ireland had their land confiscated and tens of thousands were transported to the West Indies as indentured laborers.

Those Catholic landowners who had not taken part in the wars still had their land confiscated, although they were entitled to claim land in Connacht as compensation.