Next year (1651) he was appointed governor of County Cork, and held this office until 1654. He was a parliamentary republican, dissatisfied with the rule of the army officers, and unfriendly to the Protectorate. He seems to have retired to Rostellan Castle, County Cork. In 1656 Henry Cromwell reported that Phaire was attending Quaker meetings. He does not appear to have become a member of the Society of Friends, though one of his daughters (by his first wife) married a Quaker. It is somewhat remarkable that Phaire himself married, as his second wife, Elizabeth, second daughter of Sir Thomas Herbert (1606–1682), the faithful attendant on Charles I in his last hours. The marriage took place on 16 August 1658 at St Werburgh's, Dublin. On 8 July 1659, shortly after the fall of the protectorate, the London-based Committee of Safety gave Phaire a commission as colonel of foot to serve under Ludlow in Ireland. At the Restoration he was arrested in Cork (18 May 1660), and sent prisoner to Dublin. Thence he was removed to London, and sent to the Tower of London in June. He doubtless owed his life, and the easy treatment he experienced, to his connection with Sir Thomas Herbert; Bishop Clancarty, whose life he had spared, also pleaded for him. On 2 November (Hacker had been hanged on 19 October; Huncks had saved himself by giving evidence) he petitioned the privy council to release his estate from sequestration, and permit him to return to Ireland. This was not granted, but in December the sequestration was taken off his Irish estates, and he was given the liberty of the Tower on parole. On 3 July 1661 he was released for one month, on a bond of £2,000. He was not to go beyond the house and gardens of Sir Thomas Herbert, his father-in-law, in Petty France, Westminster. On 19 July another month's absence was permitted him, with leave to go to the country for his health. On 28 February 1662 he was allowed to remove to Sir Thomas Herbert's house for three months. After this he seems to have gained his liberty. It was during this period that he made the acquaintance of Lodowicke Muggleton, whose tenets he adopted. Some time in 1662 he brought Muggleton to Sir Thomas Herbert's house and introduced him to his wife, who also became a convert. Their example was followed by their daughters Elizabeth and Mary, and their son-in-law, George Gamble, a merchant in Cork, and formerly a Quaker.