In 1649 the English soldier and statesman Oliver Cromwell landed at Dublin, which the Roman Catholic lords had been unable to take. Seeing themselves as Protestant avengers of the 1641 uprising as well as Parliamentarians fighting against the Royalists, the 10,000-strong force of the New Model Army stormed Drogheda and put its garrison of 2,000 men to the sword.

The attack on Wexford led to a similar outcome. 

Cromwell's successors, the English soldiers and regicides Henry Ireton and Edmund Ludlow, successfully concluded the war, and a great part of the best land of Munster, Leinster, and Ulster was confiscated and divided among the soldiers of the Parliamentary army. 

The Roman Catholics and Royalist landowners were banished to Connaught. A portion of the land confiscated at this time was later restored under Charles II, but at least two thirds of the land in Ireland remained in the hands of the Protestants.

The viceroyalty of Ormonde, while maintaining the Protestant ascendancy, did much to restore order and promote industry.