From the sources we learn that, in the place where the abbey of Santa Maria della Giustizia stands today, there was a hospice for the hospitalisation of the sick, mentioned in a bull of Pope Paschal II (1099-1118) as a centre for assistance to the crusaders; indeed, Taranto was one of the ports of embarkation for the Holy Land.

A “hospitium peregrinantium” known by the name of Santa Maria del Mare is attested; indeed, a documentary source informs us that in that year Constance of France, regent of the Principality of Taranto in the name of her son Bohemond, donates to the Greek monastery of San Pietro de Insula, on the largest of the Cheradi Islands, an area west of Taranto, near the Tara river, to be used for the construction of a shelter for pilgrims.

According to the scholar Mons. Giuseppe Blandamura, the change of name to Santa Maria della Giustizia derives from another document, once preserved in the Archives of the Abbey, in which a probably legendary anecdote is reported. Based on this, the Prince of Taranto Guglielmo III, who one day went to the bushes near the Tara river, came across the chapel of Santa Maria and met the guardian, the hermit Ferlizio, with whom he talked for a long time. From then on, the prince sent the hermit what he needed every day, delivered by hand by of one of his Muslim slaves named Samuel. Old Ferlizio resolved to convert that infidel (sic.), trying, every time he saw him, to educate him as a Christian. One afternoon the young man, annoyed by the hermit's insistence, killed him and, not having the courage to go back home to the prince, remained there for three days and three nights. Guglielmo, worried by the fact that Samuele had not returned, went to the sanctuary and found the body of Ferlizio; the young servant, having confessed the crime, repented and asked to be baptised, but was hung so that justice could be done. The document concludes the story about the episode thus «... omnis Civitas commota est et venit ad locum cum lacrimis vocantes eam Maria Iustitiæ et sepelierunt ambos in eodem loco», hence its new name Saint Mary “of Justice”.

The construction of the current abbey church can be dated to this period, as suggested by comparisons with the church of Santa Maria del Casale in Brindisi and that of San Domenico in Taranto.

At the behest of Cardinal G. of Aragon, the monastery passed to the monastic congregation of the Olivetan Benedictine Order, founded in the 14th century and already present in Taranto. According to the sources, to give thanks for this assignment, the doors of the church were adorned with the coat of arms of the Crown of Aragon.

In the 16th century the incursions of the Turks along the Ionian coast became more and more frequent leading to several attacks. Among these, the one that took place in 1594 at the hands of the leader Sinan Bassà Cicala, left an indelible mark on the complex, since the Turks, after having looted and destroyed the ornaments of the Olivetan abbey, set it on fire.

The now ruined abbey was abandoned by the Olivetan monks who moved to the Old Town at Santa Maria del Porto, whose remains survive under the current Spartera palace, and to the church of Monteoliveto (Madonna della Salute). The inhospitable territory, due to the swamping of the land around the Tara River, also contributed to this decision. To prevent the church from being completely abandoned, it was arranged to officiate at religious ceremonies at least on Sundays and public holidays. The Olivetan monks delegated this task to the Capuchin Franciscan friars, who officiated at the services until 1808.

The Olivetan Benedictine Order was suppressed and the abbey of Santa Maria della Giustizia definitively lost its religious prerogatives.

Following a visit from two priests, N. Mannarino and G. Cervo, who found that the complex was being used as a warehouse, Archbishop GA De Fulgare ordered the removal of the marble altar and that the fresco of Mary Most Holy be covered to avoid further profanation.

The complex of Santa Maria della Giustizia becomes Government property, and is later purchased by private citizens: the Acclavio family and subsequently the Trojlo family.

In this year the site was included among Government property and entrusted to the Superintendency for Environmental, Archaeological, Artistic and Historical Heritage of Apulia.

Restoration work on the entire architectural structure begins, re-roofing, masonry consolidation, injections of cement mixtures, which lasted until 1985, the year in which the restoration of the wall paintings, badly damaged especially following the change of the intended use of the complex and acts of vandalism, began. The restorations continue until 1993; during these works, archaeological investigations were also carried out.

The structure underwent further redevelopment works which saw the general overhaul of all external surfaces and roofing, the restoration of the former “hospitium peregrinorum” and of the refectory, the installation of new systems and further archaeological investigations.