By the early 17th century, the Lady Chapel was said to have been in ruins, and the arch at the east end of the choir was closed off by a lath and plaster partition wall.
There was also routine flooding and a series of galleries was added to accommodate large congregations.
In 1620 the English-born judge Luke Gernon referred to the cathedral's poor state of repair.

During the stay of Oliver Cromwell in Dublin, during his conquest of Ireland the Commonwealth's Lord Protector stabled his horses in the nave of the cathedral.
This was intended to demonstrate Cromwell's disrespect for the Anglican religion, which he associated with Roman Catholicism and political Royalism.

After the Restoration of the monarchy in 1660, repairs to the building were begun.

In 1666, the cathedral chapter offered the Lady Chapel for the use of French-speaking Huguenots who had fled to Ireland, and after some repair and preparation works, it became known as L'Eglise Française de St Patrick.
A lease was signed on 23 December 1665 and was renewed from time to time until the special services ceased in 1816, by which time the Huguenots had been fully assimilated into the city population.

In 1668 the roof, in danger of collapsing, was taken down, a new roof being completed by 1671.
Buttresses were erected and the west window was replaced with a perpendicular window.
Then, in the 1680s, the choir was reformed.
In 1688–90, during the Williamite War in Ireland, James II and his fellow Catholics briefly repossessed St Patrick's.
James attended Mass services there with his Jacobite supporters for a time.
However, the victory of the Protestant Williamites in this war meant that the cathedral was restored to Anglican ownership in 1690 when James abandoned Dublin after his defeat at the Battle of the Boyne.
By the early 17th century, the Lady Chapel was said to have been in ruins, and the arch at the east end of the choir was closed off by a lath and plaster partition wall. There was also routine flooding and a series of galleries was added to accommodate large congregations. In 1620 the English-born judge Luke Gernon referred to the cathedral's poor state of repair.
During the stay of Oliver Cromwell in Dublin, during his conquest of Ireland the Commonwealth's Lord Protector stabled his horses in the nave of the cathedral. This was intended to demonstrate Cromwell's disrespect for the Anglican religion, which he associated with Roman Catholicism and political Royalism.
After the Restoration of the monarchy in 1660, repairs to the building were begun.
In 1666, the cathedral chapter offered the Lady Chapel for the use of French-speaking Huguenots who had fled to Ireland, and after some repair and preparation works, it became known as L'Eglise Française de St Patrick. A lease was signed on 23 December 1665 and was renewed from time to time until the special services ceased in 1816, by which time the Huguenots had been fully assimilated into the city population.
In 1668 the roof, in danger of collapsing, was taken down, a new roof being completed by 1671. Buttresses were erected and the west window was replaced with a perpendicular window. Then, in the 1680s, the choir was reformed. In 1688–90, during the Williamite War in Ireland, James II and his fellow Catholics briefly repossessed St Patrick's. James attended Mass services there with his Jacobite supporters for a time. However, the victory of the Protestant Williamites in this war meant that the cathedral was restored to Anglican ownership in 1690 when James abandoned Dublin after his defeat at the Battle of the Boyne.
St Patrick's Cathedral, Dublin