The 1605 church of Bom Jesus, "Good" or "Menino Jesus", is known principally for the tomb of St Francis Xavier. In 1946, it became the first church in India to be elevated to the status of Minor Basilica. On the west, the three-storey Renaissance facade encompasses Corinthian, Doric, Ionic and Composite styles.

The interior is entered beneath the choir, supported by columns. On the northern wall, in the centre of the nave, is a cenotaph in gilded bronze to Dom Jeronimo Mascaranhas, the Captain of Cochin and benefactor of the church. The main altar, extravagantly decorated in gold, depicts the infant Jesus under the protection of St Ignatius Loyola; to each side are subsidiary altars to Our Lady of Hope and St Michael. In the southern transept, lavishly decorated with twisted gilded columns and floriate carvings, stands the Chapel and Tomb of St Francis Xavier. Constructed of marble and jasper in 1696, it was the gift of the Medici, Cosimo III, the Grand Duke of Tuscany; the middle tier contains panels detailing the saint’s life. An ornate domed reliquary in silver contains his remains; on his feast day, December 3, the saint’s finger is displayed to devotees.