By the time of the second siege, the military situation had turned against the Jacobites; their main force had been badly defeated at the Battle of Aughrim in July, with over 4,000 killed, including their commander, the Marquis de St Ruth, and thousands more either taken prisoner or deserted.

The town of Galway capitulated in July 1691; its Jacobite garrison was accorded 'all the honours of war,' which allowed them to retain their weapons and receive a free pass to Limerick.

After this point, Patrick Sarsfield ousted the Chevalier de Tessé and the Marquis d'Usson, the French commanders in Limerick, and began negotiations to surrender.

He and Ginkel concluded a treaty that promised to respect the civilian population of Limerick, tolerate the Catholic religion in Ireland, guarantee against the confiscation of Catholic-owned land and allow Sarsfield and the fully-armed Jacobite army to withdraw to France.

The terms of the Treaty of Limerick were not honoured by the 1697 Protestant-dominated Irish Parliament, and Catholics were subjected to the continuous oppression of the Penal Laws, which discriminated against them until the early 19th century.