In April 1588 Perrot, George Owen, his fellow Deputy Lieutenant of Pembrokeshire, and other members of the local gentry were occupied with measures to defend Milford Haven against a landing by the Spanish Armada, and in October of that year Perrot reviewed levies from Wales preparing to defend against a possible landing by the remnants of the Armada in Ireland. At about this time Perrot was also involved in a Chancery suit aimed at overturning the will of Sir Thomas Cheyne, Perrot's maternal grandfather, whose son, Henry Cheyne, had died in 1587 without male issue. The suit was not resolved in Perrot's lifetime, and was reopened by his daughter, Penelope, in 1619. In 1590 Perrot was removed from the Deputy Lieutenancy of Pembrokeshire, allegedly at the behest of Sir Christopher Hatton, who is said to have been his 'unremitting foe'. In 1591 he was again was in prison, although no charges were brought against him. In 1592 his father, Sir John Perrot, was convicted of treason and attainted, and died in the Tower of London, not without suspicion that he had been poisoned. Despite the attainder, Perrot claimed his father's estate, and by an Act of Parliament in March 1593, which was 'rushed through both Houses in four days', Perrot was restored in blood through the efforts of his brother-in-law, Robert Devereux, 2nd Earl of Essex, inheriting Haroldston Mansion and Laugharne Castle together with of the rest of his father's estates with the exception of Carew Castle, which was taken by the Crown. Perrot was a member of two committees in the 1581 session of the prorogued 1572 Parliament, although the identity of his constituency at the time is uncertain. He sat in the 1586 Parliament as Knight of the Shire for Cardiganshire. In February 1593 he was elected for Pembrokeshire. Perrot fell ill in early 1594, and made his will on 12 February. As he had no male heir, his property was divided between his wife, Dorothy, and his daughter, Penelope. Perrot married Dorothy Devereux (d.1619), daughter of Walter Devereux, 1st Earl of Essex, by whom he is said to have had a son who predeceased him without issue, and a daughter, Penelope. Perrot's daughter, Penelope, married firstly the astronomer Sir William Lower, by whom she had three sons and a daughter.