Text & photograph by Tricky Vandenberg - March 2011
The Franciscan Church was situated off Ayutthaya's city island in the southern area in Samphao Lom sub-district. The Church of the Franciscan sect was one of the three Roman Catholic churches in the Portuguese settlement; the other two being the Church of San Petro for the Dominican sect and the Church of San Paolo for the Jesuit sect. The Franciscan Church was the most northern of the Portuguese settlement, which stood opposite the Japanese village, overlooking the Chao Phraya River.
There is not much known on the Franciscan missionary work in Siam of that time. Apparently the Franciscans opened a mission in Ayutthaya in 1582, on decision of their headquarters in Malacca. Fr. Jeronimo de Aguilar was appointed vicar general of the mission and send to Siam. Shortly after a group of Franciscan fathers on the way from Macao to Europe via Malacca called by and joined the mission in Ayutthaya. The group consisted of the Father Superior Augustin de Tordesillas, Martin Ignacio de Loyola, Juan Bautista Lucarelli and Juan Probe. The group though, decided to return to Macao on account of the father superior's grave infirmity and planned to organize a more efficient missionary expedition to Siam at a later stage. 
This missionary expedition started off eight months later with the same group and joined by Jeronimo de Aguilar, Francisco de Montilla and Diego Jimenez, with the aim of providing spiritual care for the Portuguese and other Christians of different origins. King Maha Thammaracha, observing the arrival of the large group of priests, ordered a proper monastery of stone and lime built. In 1585 the monastery, called Madre de Deus (Mother of God), was inaugurated. The friary had a cloister and many dormitories (obviously with a view to train local clergy), workshops and a church.  The same year Fr. Antonio da Madalena was sent to Siam. He stayed till 1588. 
After 1588 there was apparently a period that no Franciscans friars were present in Ayutthaya, but because of the Dominican mission was abandoned for unknown reason, the Franciscans decided to re-open their mission and sent Fr. Grogorio Ruiz in 1593. 
After King Naresuan took Lovek (Cambodia) in 1594, he returned with a great number of captives of all feathers. There were captive Portuguese who were troublesome at such a point that the King forbade the Portuguese and the religious to leave Ayutthaya. The missionary activity had its ups and downs as it was influenced by the Portuguese quarrels with the Siamese. The mission was also marred by bloodshed.
On 21 March 1600, a newly baptized wife of a Japanese businessman was stabbed to death in the Franciscan church in full view of the congregation by her husband, when learning of his wife’s conversion after returning from a trip.  Father Ruiz left for Spain in 1603. Other Franciscans who continued the mission, were Fr. André do Espírito Santo (1606-1611), Fr. André de Santa Maria (1610-1616) and Fr. André Pereira. 
After the Don Fernando De Silva incident of 1624 - in which the Portuguese captured a Netherlands yacht in Siamese waters - all the Portuguese in Siam fell out of favour. In 1628 a Siamese junk was sunk by the Portuguese and at the end of that year, a state of war existed between Siam and Portugal. All this was of course not very favorable for the Franciscan mission and I presume it was left abandoned in that period.
On 9 April 1639, a Portuguese Embassy from Macao arrived in Bangkok headed by Ambassador Captain Francisco d'Aguiar Evangelho, with the aim to restore diplomatic and trade relations. He was accompanied by the Franciscan father António de S. Domingos. The Ambassador requested the Siamese King that the priest would be allowed to remain at his own account and be given the right to practice religious belief in freedom and have access to the court. He was asked also to provide a stipend of four Taels. King Prasat Thong apparently agreed with the request. 
When the French missionaries arrived at Ayutthaya in 1662, there were two Franciscans priests active, next to four Jesuits, two Dominicans, and 3 secular priests. Known other Franciscan fathers were Fr. Luis da Madre de Deos (1673-1689), Agostinho de S. Mónica and Francisco de S. Bonaventura (arrival in 1755). 
The settlement was likely destroyed during the Burmese attack on Ayutthaya in 1767.
Gervaise did not report the Franciscan Church in his work "The Natural and Political History of the Kingdom of Siam". He mentions only two Catholic Portuguese churches being the Church of Santo Domingo and the Church of Santo Paulo.  Neither Simon de La Loubère in his "A new historical relation of the Kingdom of Siam" makes a reference to the Franciscan Church. On his map he also, mentions only the churches of the Portuguese Jacobins and Jesuits. 
The area of the Franciscan Church has not yet been excavated. The location of the church is mentioned on a plan of the Portuguese settlement drafted somewhere in the eighties when the San Petro Church was excavated. The plan indicates also the location of the San Paulo Church, but after excavation of that specific area the location proved incorrect. The question remains in how far the location of the Franciscan Church would be well correct. On basis of this plan I tentatively indicated the presumed location of the Franciscan Church on the aerial picture below.
 True Confucians, bold Christians: Korean missionary experience, a model for the third millennium - Antton Egiguren Iraola - (Rodopi, 2007).  The great role of Jean-Louis Vey, apostolic vicar of Siam (1875-1909), in the church history of Thailand during the reformation period of King Rama V, the great (1868-1910) - Surachai Chumsriphan - Dissertatio ad Doctoratum in Facultate Historiae Ecclesiasticae Pontificiae Universitatis Gregorianae (Roma, 1990).  Dutch east India Company merchants at the Court of Ayutthaya - Bhawan Ruangsilp.  The Natural and Political History of the Kingdom of Siam - Nicolas Gervaise (1688) - (White Lotus 1998) page 152.  A New Historical relation of the Kingdom of Siam - de La Loubère (1691) - (White Lotus -1986).