Duffy, Patrick (d. 1675), Franciscan friar and catholic bishop of Clogher, was born in the early decades of the seventeenth century in the parish of Aghnamullan, Co. Monaghan. He was a member of a leading family of the old O'Duffy sept of Ballyduffy, Co. Monaghan, and nephew of Heber MacMahon (qv). Little is known of his education and early career, though it is likely that he first came into contact with the Friars Minor at their refuge in Chapel Moyle, Lough Egish. He spent time on the continent, and may be the Patrick Duffy listed as a student of the University of Louvain in 1634 and 1637. He was appointed confessor and preacher at the Irish Franciscan chapter held at Cavan in 1649, but subsequently returned to mainland Europe. He became assistant provincial of the Irish province in Madrid on 12 November 1655 and was elected a general definitor at the general chapter in Rome in 1664. He was the only Irish member of a committee established in 1666 to deal with Father Peter Walsh (qv), who had caused the arrest of a number of Irish priests and laymen opposed to the loyal remonstrance of 1661. Duffy secured Walsh's imprisonment for three months in Madrid for the persecution of members of Duffy's family. In October 1670 he referred to this episode when refuting charges of partiality towards Walsh.
While Duffy's attitude to Walsh reflects an anti-Ormondist stance unsurprising in one related to Heber MacMahon, his success in having the cleric arrested also indicates considerable influence with the authorities in Madrid. He was confessor to the Spanish queen and his connections with the city's political elite are reflected in those advocating his promotion: he was proposed for the diocese of Clogher as early as 1665, and the duke of Medina wrote to Cardinal Barberini on 31 January 1669 urging the Franciscan's advancement. Further correspondence from the duke requested that Duffy be honoured with the primacy of Armagh or the bishopric of Clogher. Hugh O'Neill, exiled earl of Tyrone, also favoured his promotion to Armagh, but O'Neill's intercession came too late as Oliver Plunkett (qv) had already been appointed. Nicolai Paulez, a Spanish gentleman, gave an undertaking that in the event of Duffy becoming a bishop he would provide him with an annual pension of 1,000 scudi, a pledge he did not honour. Additional support came from the nuncio in Spain, who wrote to the cardinal secretary of state in September 1669 declaring that those opposed to Duffy had defamed him. Such opponents included Plunkett, Bishop Nicholas French (qv), and catholic Anglo-Irishmen both in Ireland and on the continent.
Despite such formidable adversaries Duffy was appointed bishop of Clogher in May 1671 due to a petition received from twenty members of the diocesan clergy in October 1670 requesting it. Plunkett cast aside his hostility and pledged to defend the new bishop from his enemies, including the viceroy, Lord Berkeley (qv), who asserted that he would not let Duffy remain in the country as he believed Duffy held pro-Cromwellian sympathies. Because of Berkeley's opposition, Duffy remained in Madrid until early 1673, from where he travelled to Brussels and subsequently to London. Remaining there for a few months because of illness, Duffy made contact with the secretary of state, the earl of Arlington, whom he had previously obliged in Madrid. Reciprocating Duffy's goodwill, Arlington wrote a favourable letter of introduction to the new viceroy in Dublin, Arthur Capel (qv), earl of Essex. Its effect might have been negated by a letter from James Butler (qv), duke of Ormond, on 27 September 1673, questioning Duffy's character, but by the time it reached the viceroy Duffy had already landed at Ringsend.
A decree of 27 October 1673 ordering all prelates and regular clergy out of Ireland complicated Duffy's task, but he remained defiant, travelling in disguise throughout his diocese in the winter of 1673–4, his hardship intensified by ill health. However, he was assisted by his flock, and also had non-catholic benefactors, including the planter captain John Foster, and George Bleak, whose hostelry had previously sheltered Plunkett. A letter from Duffy to the cardinal protector in Rome, written in May 1674, described how he could not appear in public for fear of persecution and begged the cardinal for relief. His health deteriorated in the winter of 1674–5, and he died in late July or early August 1675. Duffy was buried in the parish church of Clontibret, the ancient O'Duffy burial place.