The period from 1641 to 1649 was a turbulent period in Ireland. The forces of the Catholic Confederacy struggled against the English forces, which were themselves riven by the conflict between parliament and the crown in the prelude to the English Civil War. The dispossessed merchants of Cork city, who had been expelled from the city in 1644, were briefly reinstated in 1648 when English forces in Cork declared for the Royalist side. Their reinstatement was short-lived; they were expelled again in 1649 on the arrival of Cromwell. After the defeat of the Royalists in the English Civil War, Cromwell was free to turn his attention to Ireland which he quickly and brutally subdued. His treatment of the defenders of Drogheda and Wexford still haunts the Irish folk memory. Cork city was under military governance from 1644 to 1656 after Cromwell granted a new municipal charter to the Protestants of Cork city. The municipal government of the city was to remain firmly in Protestant hands until the reform of the Corporation in the mid-nineteenth century, apart from a brief period during the reign of James II when the Old English regained control of the city.
Orders expelling the Irish from Cork city were made in 1651 and 1656. The fact that orders for expulsion were made several times indicates that none of the expulsions was entirely successful.
The shift in the balance of power in the city from the Old English Catholic oligarchy to the New English and Protestant settlers is starkly revealed in seventeenth-century documents listing the principal property owners in the old walled city. An analysis of these documents, which include the 1659 census and a civil survey of circa 1663, by the historical geographer Mark McCarthy, shows that by 1663 the New English outnumbered the Old English and Old Irish by a factor of almost two-to-one within the old walled city. In the suburbs outside the city walls, the Old English and Old Irish outnumbered the new English by almost three-to-one. Some of the Old English had properties in the city returned after the restoration of the monarchy in England but the dominance of the Old English merchant elite, which had lasted for centuries, was at an end.
The collapse of the parliamentary-based Commonwealth in England and the restoration of Charles II to the throne of England in 1660 raised the hopes of Catholics, both old English and Irish, in Ireland. Charles was acutely conscious of the need to retain the loyalty of his Protestant subjects in Ireland so his concessions to the Catholics were not as sweeping as they would have wished. Many of the newer Protestant settlers in Ireland regarded any concessions to the Catholic majority with disfavour. The atrocities committed by Catholic forces in the 1641 rebellion were fresh in the Protestant memory and Catholics, by virtue of their loyalty to the pope, were regarded as potential traitors to the English government.
The accession of the Catholic James II as King of England in 1685 served to heighten the fears of Protestants in both England and Ireland. When a son was born to James's wife in 1688, the prospect of a Catholic dynasty ruling England proved to be too much for the Protestant ascendancy in England and William of Orange, the ruler of Holland, and his wife Mary, the daughter of James, were invited to become the rulers of England. James II fled to France to seek help from his French allies. He landed at Kinsale in 1689, hoping to use Ireland as a base from which to regain his crown. Unsurprisingly, the Catholics of Cork rallied to the Jacobite cause. A Williamite army, unde the control of the Duke of Marlborough, was dispatched to Cork to regain the city for William and Mary.
Against an attack by an early-modern European army equipped with artillery, Cork city was practically indefensible, situated as it was and is in low-lying ground surrounded by high ground to the north and south. The commander of the garrison in Cork, Roger MacElligott, had been advised to burn the city and retreat to Kerry by Jacobite generals. Marlborough, who shared command of the Williamite army with the Dutch commander Wurtemberg, encamped his forces in the vicinity of the Lough. A detachment was sent under the command of Scravemoer to attack from the north side of the Lee, while Marlborough's forces attacked from the south.
Scravemoer's troops quickly gained control of the north bank of the Lee and bombarded the city from the high ground in the area. Marlborough's troops took Cat Fort, which was abandoned by the defenders after the first day's fighting on 24 September. The city was now under bombardment from both sides. Another battery set up near the Red Abbey breached the eastern wall of the city. Musketeers fired their rifles at the defenders of Elizabeth Fort from the steeple of Saint Fin Barre's Cathedral.
On the 28th of September, the Williamite army attacked from both sides of the river, supported by their artillery and by warships which had sailed up the river and joined in the bombardment. The Duke of Grafton was mortally wounded in this attack and his memory is commemorated in the street named Grafton Street in Cork. Recognising that the situation was hopeless, MacElligott, after some haggling, agreed to hand over Elizabeth Fort immediately and to surrender the city on the following day. Marlborough agreed to treat the garrison as prisoners of war and to show clemency to the inhabitants of the city. The siege of Cork was over. Its walls, which has stood for centuries, were exposed as powerless against the new weapons of war.