O'Molony, John (1617–1702), catholic bishop of Killaloe, and later of Limerick, was born probably in Kiltannon, Co. Clare. He was one of at least two sons of Thomas O'Molony and Anne McMahon of Clonderlaw, Co. Clare, his elder brother being James. His paternal uncle was John O'Molony (qv), bishop of Killaloe (1630–51). O'Molony was initially raised in Kilbogownan. From the age of 13 he resided in his uncle's household.
O'Molony was ordained a priest in 1642 by John Bourke (qv), bishop of Clonfert. He then went to be educated in the university of Paris that autumn, where he entered the ‘German nation’, one of the four houses that constituted the faculty of arts. He proved to be an excellent student and moved to the faculty of theology. He graduated with a master's degree and a doctorate of theology from there and later graduated DD from the Sorbonne. Afterwards he taught theology in Saint-Sulpice and was involved in having Irish students accommodated in the college of St Barbara. In 1659 he was appointed procurator of the German nation.
Aside from his academic activities during the 1640s and 1650s O'Molony became involved in religious disputes and politics. He was involved in successfully defending the censures of Rinuccini (qv) against the Ormond peace agreements at the Sorbonne in the late 1640s and early 1650s. He likewise took part in a dispute between the Irish students at the university of Paris and the faculty of arts over a declaration that the former had issued condemning Jansenism in 1651. Though condemned by the faculty of arts, the Irish stance was supported by the faculty of theology and the parlement of Paris. The same year O'Molony was accused of drawing up a covenant for mutual support among the Irish within the German nation; he later admitted to this. He also became attached to a canonry in Rouen during this decade, from which he drew an income, though he does not seem to have taken up residence there till 1667, at which time he resided in the bishop of Rouen's palace. This post, along with other similar appointments and a possible income drawn from land in Clare, led to his being independently wealthy. In the late 1650s he involved himself with the court of Henrietta Maria, the exiled widow of Charles I. There he became associated with Murrough O'Brien (qv), earl of Inchiquin, and frequently acted as intermediary with Ormond on his behalf. There is some suggestion that he played a role in Inchiquin's conversion to catholicism. In 1658 he was nominated as the choice of the catholic gentry of Killaloe for the bishopric of that diocese. This was supported by members of the French episcopacy.
During the 1660s O'Molony remained in France; being considered a friend of Louis XIV and Colbert. While there he seems to have actively sought military aid for Irish catholics, having some contacts with Colbert in this regard, which were brought to the attention of Ormond in 1667. In 1668 calls for his appointment as bishop of Killaloe were renewed and he was appointed bishop in 1671, being consecrated on 6 March 1672. He had to be ordered to return to Ireland by Propaganda Fide in August, which he quickly obeyed. There he became involved in efforts to end divisions between clerics, particularly between the regular and secular clergy. He was quickly considered by Lord Deputy Essex (qv) to be one of the most able of the catholic episcopate, and earned a reputation for frustrating the government policy of divide et impera towards the catholic clergy. In November 1672 O'Molony ended differences between Oliver Plunkett (qv) and Peter Talbot (qv), and dissensions between Colonels Fitzpatrick and Talbot. In early 1673 he attempted to stop a Dominican named John Byrne from accusing Peter Talbot of exercising a foreign jurisdiction. He was also nominated by the other Irish bishops to go to France and attempt to establish an Irish ecclesiastical college that same year. He later left the country in late 1673 or early 1674 at a time when Dublin Castle was seeking to expel catholic bishops, though Oliver Plunkett was to criticise him for abandoning the country so readily. In 1677, following O'Molony's efforts, the Collège des Lombards was acquired for the purpose of housing an Irish seminary. The college was established by letters patent from Louis XIV that year. O'Molony was responsible for the building of the college's chapel.
The end of the Essex viceroyalty saw O'Molony return to Ireland in 1677 with the duke of York's blessing. In the late 1670s and early 1680s his links to France led him to be suspected of complicity in the ‘popish plot’ and efforts were made to seize him. Testimonies gathered as part of these investigations led to O'Molony being implicated in schemes to acquire aid from the continent. He seems to have withdrawn into Connacht for a time in 1679 for his own safety. He remained active in his office for some time, however; in early 1681 he imposed a priest on the parishioners of Tulla against their wishes, and he was reported to be in the company of Lady Clare, a kinswoman, early that year. Faced with continued pursuit, O'Molony returned to France later that year. After his return, in June 1681, he wrote to Propaganda Fide explaining his withdrawal, commenting on the dangers he faced, stating that he was believed to be the leader of a catholic plot, and drawing attention to the £150 reward on his head, which was in contrast to the usual bounty of £10 for a catholic bishop.
The accession of James II (qv) to the throne in 1685 allowed O'Molony to return to Ireland. In 1687 he was appointed administrator of the diocese of Limerick, where he consecrated the Franciscan abbey on 24 October. On James II's recommendation he was consecrated bishop of Limerick the following year, while continuing to act as administrator of Killaloe. James made this recommendation as the papacy conceded to him the right to nominate to bishoprics. O'Molony opposed it, however, as it could have led to Englishmen being appointed to posts in Ireland. In 1689 he was to condemn the failure of the patriot parliament to repeal Poynings’ law. With the lifting of the first siege of Limerick in 1690 O'Molony returned to France with a delegation to James II, where he was to remain. His continuing popularity with the French establishment is seen in his receipt of a clerical pension throughout the 1690s. While there he continued his activities, being identified as a Jacobite conspirator by some British sources in the early 1690s. He also subscribed to a letter written by the Irish episcopate to the pope, seeking support for the Jacobite cause in 1691.
John O'Molony died 3 September 1702 at Issy, Paris. He was buried in the Collège des Lombards. In his will he left 1,200 livres for a new Irish college in Paris, 300 livres for the support of students in the Collège des Lombards, and six bursaries for Irish students in the college of Louis le Grand, with preference going to his relatives and their descendants in the matter of who obtained them.