In the 16th Century, under the Tudor dynasty, the whole territory of Ireland was re-conquered, which began under Henry VIII, and by 1603 Ireland was fully under English authority, concentrated in Dublin. The English community of Dublin, and the greater area, was happy with the disarmament of the native Irish but were not pleased with the Protestant Reformation, as they were predominantly Roman Catholic. Several citizens of Dublin were executed for their involvement in the second Desmond Rebellion in the late 16th Century, led by James Fitzgerald against the English government. The Nine Years War of the 1590s added to the discontent of Dubliners. By law, Dubliners had to accommodate English soldiers, who raised the prices of food and spread disease.

In 1592, Elizabeth I opened Dublin Trinity College, which was initially a Protestant university for the Irish gentry but wealthy Dublin families snubbed it and sent their children to Catholic universities across Europe. These factors contributed to the English authorities' changing perception of Dubliners, as they came to see them as unreliable and chose to settle Protestants from England in the city. This new class formed the basis of English administration in Ireland and remained so until the 1800s.

By 1640, Protestants had become the majority in Dublin. Thousands of them fled there to escape the bloody Irish Rebellion of 1641. This revolt began as a coup d'etat by Irish Catholics but ended in bloody attacks between Catholics and Protestants. Eventually, the English garrison in Dublin expelled the Catholics from the city. Sadly, Dublin was laid under siege in 1646 and 1649 in the Eleven Years War, but in both cases the attackers were driven off.

Later, after Oliver Cromwell took control of Ireland, during the Cromwellian settlement period, Catholics were officially banned from living within city limits, which, however, was not strictly enforced. In fact, the Catholic English community was perceived as part of the native Irish community. Toward the end of the 17th Century, Dublin became the capital of the Kingdom of Ireland, which was under the authority of the Protestant English minority; Dublin was actually among the few parts of Ireland, where Protestants were a majority. During the next century, the city expanded, becoming more prosperous and peaceful.