After the outbreak of the Irish Rebellion of 1641, the Franciscan community in Buttevant welcomed the Confederate Catholic army of Lord Mountgarret – one of the leading Catholic magnates in the south of Ireland. The guardian, Father Boetius Egan, accompanied the army and took part in the Confederate Parliament in Kilkenny in 1642. In the ensuing war in Munster, the Protestant commander, Murrough O'Brien, Earl of Inchiquin, assembled his English Parliamentarian army in Buttevant and burned the friary church. Inchiquinn's conduct in the war earned him the nickname "Murchadh na dTóiteán" – "Murrough of the Burnings". A large quantity of bones from the nearby Battle of Knocknanuss (1647) were said to have been placed in the crypt under the church choir.