The Portuguese were the first Europeans to discover the sea route to India when Vasco da Gama landed at Calicut in 1498. Two years later, on 24th December 1500, Portuguese ships under the command of Admiral Cabral visited Cochin and the Rajah of Cochin permitted them to engage in trade. In 1503 Alphonso Alburquerque was given permission by the Rajah to build a fort at the mouth of the river which was constructed mainly of the stems of coconut trees bound with iron bands, whilst the rampart of stones and sand formed the inner defence. Within the Fort they erected a church of wood which was dedicated to St. Bartholomew and which occupied the site on which the more spacious structure of the Franciscans later arose. In 1506 Dom Francisco Almeyda, the Viceroy, was permitted by the Cochin Rajah to build a new city of mortar and stone. The buildings were roofed with tiles, a privilege- hitherto confined to the palace of the local prince and to the temples in which he performed puja. The Portuguese vowed that, apart from the fortifications, the first permanent erection would be a house for Divine Worship. The new Church, was completed in 1516 and dedicated to St. Antony.

Towards the end of 1524 Vasco da Gama returned to Cochin (Which he first visited in 1502) where he died on Christmas eve of that year and was buried in this Church. Fourteen years later his remains were removed to Portugal and deposited at Vidigveria where they remained until 1872 when they were removed to Lisbon.

The Church remained in the Order of St. Francis until the arrival of the Dutch in 1663. One of the first acts of the Dutch was to order all European Catholic priests to quit their territory, after which they demolished all the convents and churches of the place, except the Church of the Franciscans which they reconditioned and converted into their Government Church. On 8th January 1664 they celebrated their first service with a parade of all arms on the Anniversary of their entry into the city. During the reconditioning the stone alter and the wiring gilded screens were removed and taken to the Church of Vypeen, which the Dutch permitted the Roman Catholics to build in 1665, and the Communion table and rostrum furniture were installed in their stead. A tablet over the west door indicates that the Church was renovated in 1779.

When the British captured Cochin from the Dutch in 1795 they permitted them to retain possession of the Church for a time. In 1804 the Dutch voluntarily surrendered the Church to the Anglican Communion when it was passed to the Ecclesiastical Department of the Government of India. But when the Rev. Thomas Norton came to Cochin in 1816 on his way to inaugurate the work of the Church Missionary Society at Alleppey, he found that the Church was just bare walls, the interior was very dilapidated and part of the roof had fallen in. The Building was sufficiently restored to enable Bishop Middleton, the Metropolitan, to use it for a Confirmation Service during his Episcopal visit to the Malabar Coast.

The change of name of the patron saint was presumably due to the Anglicans, for it was not until 1870 that any reference was made to St. Francis Church. The gravestones let into the walls of the church were taken from the floor of the nave in 1886. On the northern side can be seen Portuguese gravestones. The Dutch gravestones are on the southern wall. The Vasco da Gama stone is on the ground at the southern side. A tablet inside the building over the west door shows that it was "repaired by the Government of Madras in 1887, being the fiftieth year of the reign of Victoria, Queen of Great Britain and Ireland and Empress of India."

The Church possess an interesting link with the past in the form of the 'Doop Book' the old baptism and marriage register from 1751-1804 which may be seen in the vestry. It was maintained for 40 years in the handwriting of Predikant Cornelies and was sent to London in 1932 for the leaves to be repaired by experts. It was then rebound in the original style. A Photostat copy takes the place of the original for scrutiny by visitors.

The Church became a protected monument in April 1923 under the Protected Monuments Act of 1904. The Cenotaph in memory of the residents of Cochin who fell in the First Great War was erected in 1920 and was unveiled by Governor of Madras on October 21st of that year. The boundary walls were erected in 1924.

The Clock on this Church was erected in the year 1923 in memory of Hal Harrison Jones, a former managing director of Aspinwal. A few memorial brass plates and marble slabs were erected in the memories of very important persons who had contributed their own lives this Church and the Society. The present furniture were installed when it was under the Anglican order of worship. Now the Church is owned by the Church of South India (CSI) and there is regular worship in this church on every Sunday and commemorative days. On week days it is kept open for visitors and tourists.

• Portuguese Period: 1503 - 1663 (Roman Catholic)
• Dutch Period: 1664 - 1804 (Dutch Reformed Church)
• British Period: 1804 - 1947 (Anglican Church)
• From 1947 onwards - The Church of South India.

(The above history is an extract taken from one of the pamphlets picked up from the site, and also the photograph of the outside of the church before it was painted for the visit of the Queen Elizabeth).