During the Middle Ages, a medieval settlement developed in the area of the early Byzantine town of Stobi near Veles (Diocese of Bitola), after which the area of the settlement was used as a necropolis, while the old basilicas were partially adapted and smaller, far more modest Christian buildings were formed within their spaces.
Stobi is ne of the most important trading cities of the ancient period; One of the most significant events in the history of late antique Stobi is the formation of the Christian community. The name of the first bishop - Budia was recorded at the council in Nicaea in 325, and the old episcopal basilica also dates from the 4th century. These are the earliest documented manifestations of Christianity on the territory of North Macedonia. In 388, Emperor Theodosius visited Stobi and issued two edicts here, which forbade the assembly of heretics and public debates about religion. The discovered sacral architecture in Stobi, and especially the episcopal basilica of Bishop Philip, from the beginning of the 5th century, show that the city was a fairly significant religious center with established Christian traditions. The fact that Stobi was the capital of the province Macedonia Secunda leads some researchers to believe that it was not only a bishopric but also had the rank of a metropolitan. In 447, Stobi, like seventy other cities in the Balkans, suffered from the Huns.

Medieval horizon, basic description:
Reliably confirmed traces of life activities in the area of the early Byzantine settlement and in its immediate vicinity date to the middle and late middle ages, more precisely between the last decades of the 11th and the beginning of the 12th century and the 14th century. This horizon(s?), formed by the use of space, was recorded through stratigraphy, immovable and movable archaeological material (mainly ceramics, jewelry and coins) from the context of the settlement and with two necropolises, one in the northern basilica and the other in the Palikura basilica. During the research of the eastern rampart in 2008 and 2009, four medieval coins were found three of which belong to the coinage of Alexos I Komnenos in the period 1092-1118. There is an indication of the systematic removal of bricks that occurred at the earliest in the period 1092-1118.

Episcopal Basilica in the younger period:
On the central and northern nave of the Episcopal Basilica, also after massive demolition, a Christian building of modest size and quality was erected.

Slavic necropolis southwest of the Northern Basilica:
In the area of the northwestern part of the building of the Northern Basilica and around the central nave, burials in graves made of stone slabs were found, which appears to be the main reason for the disturbed stratigraphy in the building (23 Slavic graves). The largest concentration of graves is southwest of the basilica. All graves follow the orientation of the building and are oriented southeast-northwest. They are dated to the period of 9-10th until the 12th century. We are talking about the necropolis that extends in the area between the northern and central basilicas and probably in their surroundings. They were probably grouped around a small church, built in the eastern half of the central nave of the basilica The northern basilica in the younger period: the eastern half of the central nave of the basilica was probably adapted and used as a small church; it is not possible to date more precisely.

Archaeological findings: During excavations in 1936 of the Northern Basilica, a ring with accentuated with a head in the form of a truncated pyramid was discovered. This ring has been dated to the period between the end of the 10th and the beginning of the 12th century. On the passage between the baptistery and the northern nave, silver coins of Dragutin (1276-1282), Dušan (1331-1345), Uroš (1355-1371), Vukašin (1365-1371) and Venetian coins were found, the latest of which was minted during the reign of Francesco Dandola (1329-1339). All were placed in a silver (gilded) box of Western provenance, dated to the 14th century at the latest.

dating of the necropolis: the graves are dated to the period of 9-10. to the 12th century