Both father and son were living Duhallow in county Cork in 1641 when the Irish Uprising started. They both sustained losses. Robert assessed his financial losses during this period amounted to £51 10s. Like many Protestants he joined Murrough O'Brien, 1st Earl of Inchiquin to fight the Confederates and by September 1646 he had risen to the rank of lieutenant-colonel in the regiment of Richard Townshend. In February 1648 he was arrested, with three other officers, for refusing to join the royalist rising under Inchiquin. On 4 October these four were exchanged for Inchiquin's son, and brought to Bristol in December by the Roundhead admiral William Penn. Phaire joined the New Model Army.