Various bishops of Naissus from 4th to 6th century attended church councils and had prominent role in theological controversies of that time.

Byzantine rule in that region finally collapsed at the beginning of the 7th century and the church life was later renewed after the Christianization of Serbs.

[8] After the Byzantine campaigns of 1018 and the establishment of imperial rule in Bulgarian and Serbian lands, by the orders of emperor Basil II an autonomous Archbishopric of Ohrid was created in 1019, under the supreme ecclesiastical jurisdiction the Ecumenical Patriarchate of Constantinople.

[11] By the end of the 13th century, the city war incorporated into medieval Serbia, and the Eparchy of Niš became part of Serbian Orthodox Church.

[13] Between 1526 and 1541, during the attempt of Metropolitan Pavle of Smederevo to restore the Serbian Patriarchate, Eparchy of Niš was also included in local ecclesiastical disputes with Archbishopric of Ohrid.

In 1879, by the arrangement with the Ecumenical Patriarchate of Constantinople, Eparchy of Niš was transferred to the jurisdiction of the Metropolitanate of Belgrade.