In general, the suppression of religious houses was very much part of the Anglicisation of Ireland. A Franciscan writer of the time tells us that when James I ascended to the throne in 1603, the friars were still at Kilnalahan, but that the buildings had suffered much destruction during the recent Elizabethan wars. Protected by the Clanricarde family, the friars managed to repair the monastery and remain in residence until the end of the sixteenth century
An Act of Parliament passed in the reign of William and Mary banished all religious from Ireland. This desperate sentence left the friars at Kilnalahan with no option but to disappear. By 1710 the penal laws were relaxed somewhat and a number of friars cautiously made their way to Kilnalahan once more. There was a community of five in 1766 but by 1790 the friars had finally and forever abandoned their monastery and gardens.