This former Franciscan friary was built about 1240, only fourteen years after the death of Francis of Assisi, the founder of the order.  During the thirteenth century the friars received an annual allowance for the purchase of new habits from Henry III of England. Their habits were made from undyed grey woollen cloth, the cheapest available, and were worn as a sign of humility. A twenty five meters high bell tower with  stepped battlements was added in the late fifteenth century. The friary was dissolved by order of king Henry VIII in 1540 and, in 1544, Henry Walsh, a wealthy Waterford merchant received a charter from Henry VIII to convert it into an almshouse. This almshouse was known as the Holy Ghost Hospital. The almshouse remained on this site until 1815 when it transferred to a new location on the Cork Road. It is still in operation today and is one of the oldest charitable institutions in Ireland.

The Walshs were driven from the city during the Cromwellian period. They took up residence in the Canary Islands and became involved in the wine business. Yet despite religious differences, for many years the Protestant corporation that now controlled the city allowed the exiled Walshs to appoint Catholic masters to the hospital each time the post became vacant. 
 
In 1693, the corporation encouraged French Huguenots to settle in Waterford and establish a linen industry. The Protestant bishop Nathaniel Foy had the choir of the old friary fitted out for their religious service, hence the name the French Church. The Catholic almshouse and the Huguenot house of worship coexisted peacefully on this site for over a century. 

Among the distinguished persons buried in the friary is Sir Niall O'Neill of County Antrim, who fought for King James Il at the Battle of the Boyne and who was wounded while defending the ford at Rossnaree. He was taken to Waterford where he died shortly afterwards at the early age of thirty-two. O'Neill's monument now stands against the wall on the left-hand side of the chancel. Beneath the tower arch lies the unadorned limestone grave slab of the city's most famous architect, John Roberts.

The following extract from the Annales Minorum (vol.iii. pp.45, etc.) of Luke Wadding (1588-1657) refers to the present French church, for centuries the favourite burial place of Waterford’s leading families.  Not one of the tombs or monuments alluded to by Wadding is now to be seen, and the Lady Chapel, which was really a transept, is now separated from the church by a high wall.

"Among the very beautiful churches that adorned the city, ours was notable for the magnitude of the building as well as for the number and high standing of the friars. It was situated at the eastern side of the city, near, but inside, the walls, close to where the ships are moored.  The founder is said to have been the illustrious Sir Hugh Purcell. This is clearly proved by a portion of an ancient MS. belonging to the convent, on which is written: ‘At the right hand of the High Altar is the burial place of Sir Hugh Purcell, Knight, who was founder of this convent.’ The church is divided into two parts. The principal [part] is opposite the doorway, and may be all seen from the entrance. The second, which is smaller, but yet of a respectable size, is at the right hand as you enter, and is called the Chapel of the Blessed Virgin Mary. In this monastery, I am of opinion, lie the remains of John of Waterford, who, according to that ancient author, Pisanus, was remarkable for the greatness of his miracles, the infirm being healed, and even the dead raised to life at his tomb. Here also, the same writer tells us, was buried Nicholas of Waterford, who foretold the day of his death to his brethren. In a secret place, hidden away, was interred Brother John Luker, a man of pious and saintly memory in the city.  His body was exhumed, after many years, by one of his associates, a pious secular priest, and a most religious matron, and translated by night from the Church of St. Mary to that of his own Order, as he had requested when dying.  I was then a stripling, and was present by accident. His body, I was told, was found in perfect preservation, with his habit and sandals uninjured. Here also rests Brother Donagh Daly, who, in the years of his vigour, bore many afflictions for the Catholic Faith, and was professed in the Franciscan Order before his death. He left behind him, in the whole kingdom, a high opinion of his admirable integrity, singular prudence, and praiseworthy innocence. He died in 1614, and many things worthy of record could be written of him...

In the larger chapel, on the Epistle side, rested the bodies of the most illustrious Lord Richard Poer, Baron of Curraghmore, an active defender of the Catholic Faith, and his wife, the no less illustrious Lady Catherine de Barry, daughter of Viscount Barrymore of Buttevant. On the Gospel side, in the tomb of the founder, was recently interred Sir Nicholas Walsh, Knight, one of the chief judges of the kingdom in the Court of Common Pleas. In the large chapel of the second church, or the Chapel of the Blessed Virgin, are the tombs, of carved stone, belonging to the most illustrious Barons of Dunhill and Kilmeaden, founders of the chapel. In the centre of the same chapel, at the right hand as you enter, that is, at the Epistle side, rises, in the form of an arch in the wall, the tomb of the Waddings.

Here was buried, in my own recollection, the illustrious Sir Thomas Wadding, my own most excellent uncle, whose memory is in benediction, and will ever remain so, among his fellow citizens. He was most generous to the poor, ever ready and open hearted in offering hospitality to pious people and ecclesiastics, and discharged the most onerous duties of the Christian State. Somewhat lower down lie another uncle of mine named William, and my pious father, Walter, to whom I owe much more than my birth, a diligent care in giving me a Catholic training and the most constant watchfulness over my education. Such was the size of the church that, on the suppression of the religious houses, an asylum [The present Holy Ghost Hospital] was erected in the centre of it on beams placed across from wall to wall. In the meantime the friars live in concealment in rented houses. They assist the Catholics in every good work, though often are they sought after, even unto death. On two occasions the vice-governor of the city, an English soldier, acting under instructions from the President of Munster, burst into their place of refuge, at the south side of the town, near St. John’s gate, but they had been forewarned of the danger, and escaped his hands.”

Acknowledgment is due to Canon Power's translation into English of Luke Wadding's Annales Minorum (vol.iii. pp.45, etc.)