To the west of the Se Cathedral is the former palace of the Archbishop that connects the Se Cathedral to the Convent and Church of St. Francis of Assisi. The structure is built of laterite blocks and is lime-plastered.
The church faces west and has a nave with three chapels on either side, a choir, two altars in the transept and a main altar. To the north of the main altar is a belfry and a sacristy. The convent, which forms an annexure to the church, now houses the Archaeological Museum.
The exterior of the Church is of the Tuscan Order while the main entrance is in Manuline style. The main altar is Baroque with Corinthian features. There are no aisles but only a nave, which is rib-vaulted.
The internal buttress walls, separating the chapels and supporting the gallery on top, have frescoes showing intricate floral designs.
In a niche on the façade, stands a statue of our lady of miracles brought from Jaffna in Sri Lanka. A wooden statue of St. Francis of Assisi adorns a pedestal bearing the insignia of the Franciscans. A wooden pulpit, richly carved with floral designs is to the left as one enters.
Beneath a ribbed vault with frescoes showing floral decorations, is the main altar, which is gilded and has a richly carved niche with a tabernacle supported by the four evangelists.
The tabernacle was used for displaying the holy sacrament. Above the tabernacle, in the main altar, is a large statue of St. Francis of Assisi and an equally large statue of Jesus on the cross. Beneath the two figures are inscribed the three vows of the Saint - poverty, humility and obedience. On either side of the main altar, in the nave, are beautiful large paintings on wood, depicting scenes from the life of St. Francis of Assai.
The origin of this church and the attached convent can be traced to the humble beginnings made by eight Franciscan friars, who, on their arrival in 1517, secured from the then Governor a few houses that belonged to a deceased Thanadar. By their persistent efforts they constructed a small chapel with three altars and a choir.
A church consecrated to the Holy Ghost was built in 1521 and was later pulled down and the present church was built on the same spot in 1661 retaining only the entrance of the earlier church.