In 1549, the Church of England was changed again, this time by King Edward 6th. Across Europe a large number of Roman Catholics, led by a German priest called Martin Luther, were protesting against the corruption in the Roman Catholic church at the time. Their protests and actions became known as the Protestant Reformation, and their followers were nicknamed 'Protestants'. King Edward became very interested in the Protestant movement. He felt that the Church of England was still too Roman Catholic and ordered that confession, processions and the doctrine of transubstantiation be removed. Thus the Church of England became much more similar to the new Protestant churches that were appearing all over Europe. Most Irish refused to accept these changes to the church, not least because the new rules were written in English whereas they could only speak Irish. Therefore Ireland remained Roman Catholic while England gradually became more and more Protestant.

When Queen Mary, a Roman Catholic, came to the throne in 1553, she repealed the anti-Rome laws and made England Catholic again. This was welcomed by the Irish, but Mary did not seem to regard her common religion as any reason to treat Ireland any more kindly than her Protestant predecessor. She sent her army into what is today counties Laois and Offaly (west of Dublin) in 1556 and forcibly removed most of the native Irish from the area and gave it to English (and mainly Catholic) settlers. For 50 years, the Irish who had been removed relentlessly attacked the settlers and it wasn't until 1600 that the attacks faded away.

In 1558 Queen Elizabeth 1st came to the English throne and made England Protestant again. Although she was funding colonies in the vast, newly discovered, land to the west across the Atlantic she still regarded Ireland as a much more convenient place to colonise, being so much closer and of similar climate to England. Her reign was dogged by rebellions in Ireland. An attack by the O'Neills of Tyrone was defeated in 1561 and two revolts by the FitzGeralds of Cork and Kerry were put down in 1575 and 1580 respectively. Elizabeth took advantage of the defeat of the FitzGeralds in Cork and began a plantation in Munster. Promising people the same kind of wealth that people were finding in the Americas, many English came and settled in what had been FitzGerald land. The land was quickly farmed, towns developed and the colony was prospering by 1587. However, the colony was devastated in 1598 by a co-ordinated Irish attack from which it never recovered, although many English remained in isolated areas.