In what is considered one of the most brutal incidents of the war, survivors of the Catholic garrison were executed along with a number of civilians and the castle was sacked.

In 1642, most of the province of Munster had fallen to Irish Catholic rebels with the exception of Cork city and a few towns along the south coast, which remained in the hands of Protestant settlers.

The political and military situation was further fragmented by the First English Civil War in which the Catholics gave their support to Charles I, and the Protestants after 1643 to the Parliament of England.

A deep rift developed within their ranks in 1647 between those who were prepared to accept a mere toleration of Catholicism in return for an alliance with the English Royalists and those who in effect wanted Ireland to be a Catholic kingdom, albeit under the sovereignty of the Stuart monarchy.

This infighting was to fatally hamper the war effort of the Confederates in Munster and make possible the Protestant sack of Cashel.

Even worse, while the Munster Army was paralysed by the intrigues of its commanders, Inchiquin's Protestant forces had embarked on a highly destructive campaign in Confederate-held territory.

This provided him a secure base for raiding the surrounding countryside, largely unopposed by Lord Taaffe, probably the result of the political scheming of Muskerry and other powerful Irish clan chief who hoped to keep the Munster army intact for their own ends.

For another half an hour, fighting raged inside the church, until the depleted defenders retreated up the bell tower.

The slaughter of the garrison at Cashel and the subsequent devastation of Catholic-held Munster earned Inchiquin the Irish nickname, Murchadh na Dóiteáin or "Murrough of the Burnings".

[8] The political ramifications in the Irish confederation were also profound, serving to exacerbate the split between the Catholic party headed by Giovanni Battista Rinuccini and those sympathetic to the Royalist lord Ormonde.

When he did so in November, the politically divided and badly led Munster army was routed and destroyed at the Battle of Knocknanuss.