Archaeological investigations were undertaken at the same time as restoration work conducted under the supervision of the Superintendency, in the crypt of the Romanesque cathedral. These investigations were able to complete the exploration of the archaeological area partially uncovered in the 1960s and 70s. The remains of a large imperial Roman building were uncovered. It comprised several rooms and was characterised by the use of large ashlar blocks of calcarenite. Also preserved was a patch of mosaic pavement dating to the 1st century A.D., made of limestone tesserae, cobbles and terracotta, with a large motif of interlaced circles delimiting rosettes with six petals.

Adjacent to this building a stretch of paved road came to light which could hypothetically be identified with the urban route of the via Traiana. An interesting find was an honorary inscription on a marble slab, reused in a subsequent period, presumably belonging to a lost statue base. Dated to the second half of the 2nd century A.D. it was dedicated to a priest of Augustus, Lucius Gellius, who had been granted the honour of a bisellium and a statue by the decuriones.

The Roman remains were overlain by the structures of a large early Christian basilica, 40 m long and 18 m wide, with three naves and the apse facing east. As well as the structures belonging both to the perimeter walls, in some places preserved to a height of circa 3 m, and the walls on which the pilasters dividing the naves rested, large patches of a polychrome mosaic were visible, particularly in the crypt, known as “the mosaic of Timothy”. Created in several phases, datable to between the 5th and 6th century A.D., here the mosaic appears as a large carpet with a background motif of scales into which is set a large disc with a central square with a woven pattern, surrounded by a long sinuous ribbon. The mosaic carpet, surrounded by a mosaic border decorated with fish, aquatic animals and vegetal motifs, is characterised to the east by a large tabula ansata with a Latin inscription which tells of a certain Timothy who, in the period of the bishopric of Andrea, commissioned a part of the decoration in order to fulfil a vow.

The basilica, which constitutes the earliest cathedral at Bari, dedicated to S. Maria, remained in use in the centuries following the early Middle Ages. In 1034, bishop Bisanzio decreed its demolition and gave the order to begin the construction of a new cathedral. This was raised by circa 5 m with respect to the preceding basilica, whose structures, partially demolished, were in part incorporated into the new foundations, whilst the precious floors perhaps remained partially visible in the crypt of the new cathedral. During the 15th-18th centuries the subterranean areas of the Romanesque cathedral were used as burial chambers destined for the important families of the town.