In the heritage precinct of Old Goa, there are several buildings from the Portuguese Era. At its peak, Old Goa was called "Rome of the East." Today, the monuments of Old Goa are a UNESCO World Heritage Site.

A short distance west of Se Cathedral stands a church and the Convent of St. Francis of Assisi. It is said that eight Portuguese Franciscan friars arrived in Goa in 1517 and secured a few houses from the then-governor. Eventually, they converted the houses into a chapel with three altars and a choir.

Later, the chapel was modified into a church in 1521 and consecrated in 1602. Later in 1661, the building was replaced by the current structure. The church has retained its earlier entrance as well as its original Portuguese Manueline architecture. The exterior is Tuscan, while the interior is Baroque with Corinthian features.

During the 1830s, the Portuguese banned all religious orders in Old Goa, and the buildings slowly fell into disrepair. In 1964, the convent connected to the church was converted into a museum by the Archaeological Survey of India.

The church’s interior is decorated with paintings and frescos, depicting the life and times of its patron saint Giovanni di Pietro di Bernardone, also known as St. Francis of Assisi, who founded the religious order of the Franciscans.