The origins of the Santa Scolastica monastery have been lost in the mists of time. It is certain that a settlement has existed there since the Bronze Age, as demonstrated by the discovery of the remains of a hut under the bastion wall. However, it is believed that the building itself was constructed before 1000 AD. The Bari historian Beatillo dates its origin to the year 755 AD, the Carolingian era under Popo Stefano II. This theory is supported by the fact that the Benedictine monastery SS. Trinità, considered the “father” of Santa Scolastica monastery, had already been built by 1053. In that year, an edict by Pope Leo IX named the monastery after the abbot Marco. In 1081, it was decided to erect a church dedicated to saints John and Paul in the area near the northern part of the city walls. The remains of this church were discovered under the Aragonese bastion wall which today forms the entrance to the Archaeological Museum. Some of the external and apse walls are still visible, along with the pedestals of the nave dividing pillars and, above all, the splendid inlaid calcareous paving, set out in geometrical shapes. The Benedictine nuns of Cassino settled here in 1102 and the Santa Scolastica convent was dedicated under the guide of the Abbess Agnese. At the time, the church was divided into three naves with a central apse. In 1120, dormitories and a cloister were added and the building was significantly extended and improved under the Abbess Guisanda Sebaste. Her marble tomb, re-carved from an ancient Roman sarcophagus, was located in the Refectory.
In 1156, the convent structures were some of the few public buildings to survive the destruction ordered by William the Bad, thanks to the intervention of Giorgio Maione, an admiral in the service of the Norman king and brother of Eustochia Maione, the Abbess at the time. The Abbess Marina increased the number of nuns at the convent; the donations of novices from the wealthiest families in the city greatly enriched the assets of the convent. Among its priceless treasures was a silver relic containing the arm of the apostle San Mattia, part of the plunder from the raids on Constantinople in 1204. After the presentation ceremony of the relic on 6th June 1207, it was held that the saint carried out a series of miracles. The most astonishing was the snow and water which fell on the monastery on 5th August following a long period of drought. The convent was later confiscated from the Cassino Benedictines after the unification of Italy. It underwent a series of alterations in the 19th and 20th centuries and suffered serious damage during the Second World War. Its first restoration work was carried out in the 1970s, during which the original convent buildings came to light. However, the most important restoration work was that started in 2011 and still in progress. This has led to the discovery of valuable archaeological relics from the earliest periods of history.