Ó Maolchonaire is born in the townland of Figh, civil parish of Tibohine, barony of Frenchpark, County Roscommon. His father and mother are Fíthil and Onóra Ó Maolchonaire. Two other sons survive to adulthood, Maoilechlainn and Firbisigh. They belong to a well-known family of historians and poets. He is brought up in the family profession.
Ó Maolchonaire studies for the priesthood at Salamanca, entering the Irish college founded in 1592. He first studies the liberal arts and philosophy. In 1593 he translates into Irish a short Castilian catechism by Jerónimo de Ripalda SJ. The original is a simple catechetical work written in Aristotelian master-pupil dialogue. According to Mícheál Mac Craith, Ó Maolchonaire’s translation pointedly refers to the Irish as Eirinnach rather than Gaedheal.
After five years at the Salamanca Irish college, Ó Maolchonaire leaves to join the Franciscan province of Santiago. Aodh Mac Cathmhaoil is among his classmates in the Salamanca Franciscan friary. They and nine of their peers in the Santiago province are later raised to the episcopacy, an unprecedented development in the history of the order.
At the height of the Nine Years’ War, Ó Maolchonaire sails to Ireland where he serves as a confessor and preacher to troops under the command of Hugh O’Neill and Hugh Roe O’Donnell. In 1601, they request a bishopric for Ó Maolchonaire “in recognition of his diligence, commending his sound judgment on Irish affairs.” After the disaster of Kinsale in 1601, he accompanies O’Donnell to Spain as his confessor and adviser, hoping to see a renewal of Spanish military intervention in Ireland.
In 1602, Ó Maolchonaire attempts to get approval for O’Donnell to meet Philip III in person but they are kept at arm’s length by the Spanish court. During this time, they also drafted an official complaint against the Jesuit superiors of the Irish college at Salamanca over presumed discrimination in favour of Old English students at the expense of students from Connacht and Ulster.
While waiting for a response to his repeated calls for military support in Ireland, O’Donnell becomes seriously ill and dies at Simancas, being assisted on his deathbed by Ó Maolconaire. In keeping with his patronage of the order of friars minor in Donegal, O’Donnell is buried in the Franciscan habit. Ó Maolchonaire accompanies the remains to their last resting place in the Franciscan church at Valladolid. He continues to press for military support after O’Donnell’s death. He participates in an abandoned maritime expedition which reaches Achill Sound in 1603 but never lands in Ireland. He subsequently assists the Spanish councils of state and war to stem the flow of Irish military migrants and their dependents in Spain.
As adviser to Puñonrostro, the king’s appointee as protector of Irish exiles in Spain, Ó Maolchonaire helps to secure funds for widows, orphans and clerics. Trained as a chronicler and genealogist, he sponsors the entry of Irish soldiers into Spanish military orders and successfully calls for the promotion of Henry O’Neill, second eldest son of the earl of Tyrone, as colonel of Irish infantry units in Flanders, the O’Neill tercio in 1604.
In 1606, the Franciscan general chapter is held in Toledo where Ó Maolchonaire is selected as minister-provincial of the Irish friars minor. The most notable act of his tenure as provincial is the founding of a new Irish Franciscan college at Leuven in the Habsburg Netherlands. A year before his appointment, he begins his efforts in earnest with an appeal to the Spanish king. The loss of five Franciscan houses during the Nine Years’ War makes a new foundation essential. In response, Philip III instructs Albert VII, Archduke of Austria, to provide a perpetual grant for a new college in the university town of Leuven. Ó Maolchonaire’s part in founding the college clearly influences the Catholic pastoral mission to Ireland during the seventeenth century. The first and most active Irish printing press on the continent is long in operation at Leuven.
After Hugh O’Neill and Rory O’Donnell leave Ireland in 1607, Ó Maolconaire accompanies them from Douai to Rome as interpreter and advisor. Christopher St. Laurence, baron of Howth, implicates him in a plot to seize Dublin Castle and raises a new rebellion just before the Flight of the Earls. In recognition of his losses, Philip III and Paul V offer O’Neill the concession of Ó Maolchonaire’s promotion to the archbishopric of Tuam. On Sunday, May 3, 1609, he is consecrated archbishop by Cardinal Maffeo Barberini in the centre of Rome at the Chiesa Santo Spirito in Sassia. He remains in Rome until his appointment as archbishop of Tuam before returning to Madrid on behalf of Hugh O’Neill.
In response to the 1613–15 Parliament of Ireland, Ó Maolchonaire writes from Valladolid a remonstrance to the Catholic members of the parliament, rebuking them for assenting to the bill of attainder that confiscated the estates of O’Neill, O’Donnell and their adherents. As Archbishop of Tuam, he never takes possession of his episcopal see, governing through vicars general. He continues to live in Madrid and Leuven, as is the case with many Irish clergy at the time. Like his fellow-Franciscan, Luke Wadding, and Peter Lombard, Archbishop of Armagh, he serves as a key intermediary and his influence in Irish matters is considerable. In 1626, a year after Charles I declared war on Spain, he makes the case for an invasion of Ireland under the joint leadership of the earls of Tyrone and Tyrconnell.
Ó Maolconaire dies at the Franciscan friary of San Francisco el Grande in Madrid on November 18, 1629. In 1654, two Irish friars bring his remains back to St. Anthony’s College in Leuven where he is buried near the high altar in the collegiate chapel.