The former convent complex of San Francesco della Scarpa is located near the old city of Bari, in an area adjacent to the Adriatic Sea to the northwest. Archaeological research carried out during the restoration in the 1970s demonstrated an early anthropisation of the area. Investigation in the apsidal vault of the church revealed traces of a Bronze Age hut settlement, a burial ground datable between the Archaic and Classical periods (6th-5th century B.C.), and the remains of a living quarter of the Roman city, with phases from the Republican and Early Imperial periods.
In 1220, the Dottula family donated the prayer place of St Catherine to the Friars Minor, including a large area that would become the base of the convent. The church, dedicated to St Francis, was built as an extension of the chapel of St Catherine, the work, interspersed with long periods of standstill, was completed between 1306 and 1321. The iconographic structure of the church, with a single nave, originally with a wooden truss roof, includes the choir, covered by a ribbed, ribbed cross vault of squared stone, with four angular columns above which are placed capitals, differing in style and decorative and phytomorphic details. Connected to the hall were two rooms on the left side of the apse, both with raised cross vaults, marked by ribs resting on four shutters.
The chapel of St Catherine, included in the new religious building on the right side of the apse, was intended for the raising of a bell tower, of which only a few traces remain today. With the arrival of the Angevin-Doubet dynasty (1380-1442), work resumed, allowing for the construction of a wing adjacent to the sacristy, developing from south-east to north-west. The building included an oratory and a refectory with a kitchen. In 1436, the friars of the Order of the Observant Friars Minor arrived in Bari, and from then on, the Observant (clog-wearing) and Conventual Friars Minor were distinct.
Construction of the four-sided cloister began in 1511. After the 1631 earthquake, the restoration was officially celebrated in 1672, with the reconsecration of the rebuilt church. In 1715, St Catherine's chapel was also restored and adapted for the elevation of the bell tower. With the beginning of the military use of the complex, first by the French (1798-1815), then the Bourbons (1815-1860), its decline began. With the Unification of Italy, after being assigned to various confraternities, the building continued to be used for military purposes, until 1943, when it was requisitioned by the Allied military command to house British troops. On 9 April 1945, it was badly damaged by the explosion of an Allied cargo ship and was later used as a collection centre for refugees.