The earliest record this church dates from 1442. In 1571, the church of San Martino, which stood one kilometre south of the riverbank, was destroyed by flooding and a more secure location was chosen for the present church.

Another flood in 1654 demolished the nearby rectory of San Giovanni Battista, so the inhabitants were united in a single parish and the prebend passed to the parish of San Martino with the obligation to erect an altar to St John the Baptist in the church.

In the early 18C, the minister decided to demolish the old church and build the present one, completed in 1765. Following the suppression of the convent of the Augustinian friars of San Nicola in 1786, the earlier dedicatee, St Martin, was joined by Saint Nicolas of Tolentino.