He saw service in France under the Earl of Pembroke, being present at the capture of St. Quentin. Later on he had a violent disagreement with his old commander, owing to his refusal to assist the latter in persecuting Welsh Protestants. A life-enduring friendship was later established between them by Pembroke's magnanimity in rallying to his support at a crucial period in his career. When Protestantism, at a later period, gained the upper hand under Elizabeth, he was equally averse to the persecution of Catholics. Elizabeth upon her accession continued the favours shown him by her predecessors. He was selected as one of four gentlemen to carry the canopy of state at her Coronation, and was appointed Vice-Admiral of the seas about South Wales. In 1570 he was made President of Munster, where he performed his duties in an extremely strenuous manner. He used deputies only in clerical matters; where there was fighting to be done he was there in person, and usually in the thick of it. Much as he liked to command he never could resist being in the actual scrimmage. He challenged James Fitmaurice Fitzgerald, the rebel leader in Munster, to single combat, which the latter prudently refused; later on, Fitzgerald led him and a small body of men into an ambush where he was out-numbered ten to one; Perrot refused to surrender, and though he made great slaughter of his assailants, was saved only by the timely arrival of a small body of his own men, whom the rebels supposed to be the advance guard of a stronger force. He was as generous in victory as he was imprudent in action; having defeated and captured Fitzgerald, he forgave him and restored him to his property. Such actions on his part being criticised by the Council, Perrot, in dudgeon, resigned his command and returned to England in 1573. He was received favourably by Elizabeth, whose goodwill he still continued to keep in spite of his numerous enemies at Court. Retiring to his Welsh estates at this time, he told Burghley that he intended thereafter to lead a "countryman's life," and "to keep out of debt." Much of his time during the following ten years was spent in suppressing piracy on the seas in his capacity of Vice-Admiral and Warden of the Marches. In 1584 he was appointed Viceroy of Ireland, an office which he executed vigorously and effectively, but in the same dominating spirit and with the same impatience of control that had marked his earlier Irish career. Exasperated at the delays of the Council in agreeing to his plans, he even went to the length of addressing the English Parliament in a letter, which, however, was suppressed by Walsingham, who apprehended the resentment of Elizabeth at such an unwarranted appropriation of her prerogative.
While Perrot's physical proportions were much above the average he was an extremely graceful and handsome man. A German nobleman of the time, visiting Ireland, seeing Perrot at the opening of Parliament, declared that though he had travelled all Europe he had never seen any one comparable to him for his port and majesty of personage.
Perrot's arbitrary and dominating manner created constant friction in his Council and aroused the enmity of his coadjutors and subordinates. He challenged Sir Richard Bingham, President of Munster, to a duel, and came to actual blows in the council chamber with Sir Nicholas Bagenal. He aroused the deadly enmity of Loftus, Archbishop of Dublin, who set many plots on foot to work his undoing. One Philip Williams, a former secretary of Perrot's, was set on by Loftus to make revelations reflecting on Perrot's loyalty, which gained such credence that they resulted in his recall to England in 1588. He left behind him, writes Sir Henry Wallop, "a memory of such hard usage and haughty demeanour amongst his associates as I think never any before him in this place hath done." After Perrot's return to England, Loftus continued his machinations against him. Informers of all kinds were forthcoming to accuse him. One Denis O'Roughan, an ex-priest, offered to prove that he was the bearer of a letter from Perrot to