Perrot's unsparing criticism of his associates in government made him numerous enemies. His plan for the conversion of the revenues of St. Patrick's Cathedral to fund two colleges led to a sustained quarrel with the Archbishop of Dublin, Adam Loftus, which Perrot wilfully aggravated by his interference with the prelate's secular authority as Lord Chancellor. He also interfered with Bingham's government of Connaught; caused the council secretary Sir Geoffrey Fenton to be imprisoned for debt; and in May 1587 was accused of striking the elderly Knight Marshal, Sir Nicholas Bagenal, in the council chamber, an incident his enemies blamed on his drunkenness. In January 1588 Elizabeth granted Perrot's request for recall. Six months later, at the height of the Armada emergency, he was succeeded by Sir William Fitzwilliam.