The title “St Mary of Jesus” was coined by Blessed Matteo Giummara da Agrigento (c. 1376-1450). He was an itinerant preacher who headed the Franciscan reform of the Osservanza (began by St Bernardin of Siena) in Sicily. The title came from the Marian devotion of the people where they founded the first convent, in Messina, and the Christ-centred preaching of Blessed Matteo.
On 29th March 1478 the Franciscan brother Philip (Frati Filippu), from Sicily, was authorised to come to Malta and assess the possibility of erecting a convent in Malta. Brother Philip came to Malta but it seems that the conditions were not favourable because the noble people requested Papal intervention. On 7th November 1482 the Papal Bull Pia Fidelium orders the erection of a Franciscan Convent de Observantia “as the people had requested”. In the meantime, in 1487, the Franciscan Chapter in Sicily decreed that no new convents should be founded and therefore things were officially put on hold. On 6th April 1492, Giacomo Ħakim, a noble person from Mdina, left a considerable sum of money to his brother Mariano Ħakim, a Franciscan brother who resided in the Convent of St Mary of Jesus, in Messina. The money was specifically intended for the building of a convent in Malta dedicated to St Mary of Jesus. The land was bought on 13th September 1497. It is understood that a group of friars was resident by 1504, when they commissioned a statue of St Mary of Jesus from Antonio and Domenico Cagini. This statue can s still be seen in the Church.
The social situation remained precarious and in 1506 because brother Cherubino, responsible for the friars in Malta, was instructed by his superiors to close the convent due to serious threats of invasion. The friary was not closed, however. On the contrary, more friars were sent to the Observant convent of St Mary of Jesus in Rabat tal-Imdina. In 1731 the chronist friar wrote that the convent was “a very humble abode, according to the custon of that time, in which there was one dormitory, a few cells, a cloister and a refectory.”
The Franciscan church and friary have an important place in Hospitaller history since the first Grand Master in Malta, Fra Philippe Villiers de L’Isle-Adam († 1534) maintained a room in the friary despite having his palace in Fort St Angelo.
The first Grand Master in Malta, Fra Philippe Villiers de L’Isle-Adam († 1534) was one of the earliest benefactors. He donated money for the construction of the cloister (internal yard), which is still present today. He died in one of the cells above the cloister and a commemoration stone was laid. His interiors were buried in the Church of St Mary of Jesus, (an inscription exists on the left side of the Church), his heart was sent to France, while the rest of his body was buried in St Anne’s Chapel in Fort St Angelo. Connection of this Church with the Order of St John remained and in 1557 another Grand Master, Claude de la Sengle, had his interiors buried here as well. In 1615 Grandmaster Adolph de Wignacourt wished that the interiors of his brother be buried in this Church and left a large sum of money for the celebration of Masses for his repose.
In 1693 a strong earthquake seriously damaged the building. Restoration works took a long time to start due to lack of funding. Consolidation works started in 1752 and came to an end in 1757. The present balcony for the Church organ was built in 1804, after a donation given by the Brotherhood of St Joseph as a recompense to the friars who gave them part of the convent’s garden for the Oratory of Joseph.
From Ta’ Gieżu Church the route continues past the Domus Romana (Roman Villa), through the Greek Gate in the Mdina Ditch to the piazza of the Cathedral of St Paul in Mdina.