The story of the foundation of the monastery willed by the king of the Franks, Pepin, in 755 seems to be legendary, while the first document mentioning the monastery is da- ted 1102, suggesting the monastery already existed in the previous century. In the mid -11th century the only religious building standing on the site was the church whose remains can be seen today inside the 16th-century Bastion and which can be considered the founding nucleus of the Benedictine monastery. The changes and extensions made to the monastery were carried out by the abbesses who ruled the religious community.
The most important extensions were carried out on the three sides of the original church at the beginning of the 12th century under the rule of Guisanda Sebaste: on the western side a long porticoed area identified as a dormitory, today reserved for the section “Archaeology of Bari” (see The porticoed room); on the southern side a long building placed transversally separating the monastery from the city, towards which the facade of a new church was also oriented; while on the sea side the monastery was provided with buildings architecturally more refined. The burial ground of the monastery extended mainly in the western section, and also towards the south, along the porticoed room.
A further extension is documented at the beginning of the 14th century by the epigraph located next to the current entrance, where the works requested by abbess Romana Casamassima are mentioned. They refer to the bell tower and the church, the latter located in the southwestern corner of the enclosure since the early 12th century (current building dedicated to Santa Scolastica).
After a period of crisis, between the 1400s and the 1500s, the monastery was enriched with new buildings while older buildings were no longer used. The duchess Bona Sforza was responsible for the erection of the defensive bastion on the northeastern side of the monastery (see The Bastion) and for the reinforcement of the walls. The buildings overlooking the walls were demolished in order to allow the construction of ramps and rampart walkways. The reconsecration of the monastery church in 1579 can be considered the final act in this first phase, which was followed by a fire that caused significant damage to a third of the complex.
The long restauration works extended until the mid- 17th century, at the end of which the parlatory (fig. 9) was built.The parlatory can be identified with the one willed by archbishop Ruffo in 1684. While the monastery is depicted in the 17th century views (fig. 6) as one of the largest and most important monasteries of Bari, a quick process of decay is noted at the be- ginning of the 1800s. In 1864 the monastery is referred to as abolished. The construction of the Liceo Cirillo in 1817 first and then of the consortial hospital in 1887 in the near- by convent of S. Pietro determined the latest works.
Transformed into an almshouse and later abandoned, the monastery of S. Scolastica underwent first restoration works in 1971. After becaming property of the University of Bari the monastery was valued as a possible home to the collections of the Archaeological Museum of the Province of Bari.