The Byzantine Co-Emperor Michael IX Palaiologos mentioned the Monastery of Saint Nikita near Skopje in the years 1299/1300 (πλησίον [τῶν Σκοπίων] εὑρίσ[κετ]αι μοναστή[ριον εἰς ὄνο]μα τιμώμενον τοῦ Ἁγίου μεγαλομάρτ[υ]ρος Νικήτα). In 1299/1300 or 1308 a Serbian version of a charter by Andronikos II Palaiologos - at the instigation of the Serbian King Stefan Uroš II Milutin - confirmed the donations made by Michael IX (ō priloženi ježe vь Skopi cr(ь)kva S(ve)t(a)go m(u)č(e)nika Nikiti vь metohiju).
It could well be that the scribe of the aforesaid Slavonic charter localised the Monastery of Saint Nikita wrongly in the vicinity of the Upper Town of Skopje, while it is to be found to the NW outside of the town, which is indicated by the Byzantine charter. The forged Transcript A of the Collective Charter of Stefan Uroš II Milutin for the Chilandar monastery reports that the deserted Monastery of Saint Nikita was found and re-erected by the Serbian king (I ōbrěte kraljevьstvo mi manastyrь zapustělь vь Skopʼskoi straně Svetago Nikitu ōtьčьstva mojego i napravihь jego). He donated it afterwards to to Tower of Hrusija near the Chilandar monastery (a Svetago Nikitu dahь mojemu pirʼgu sь vʼsěmь jego utʼvrьždenijemь).
The Church has an elongated cross-in-square plan, with a dome and interior which is divided into nine bays. The four bays that form a cross are barrel-vaulted. The calotte of the dome (made of brick) rests upon a high octagonal drum. The specific design of the sanctuary, which consists of the eastern arm of the cross, a short narrow bay and a semicircular apse, was imitated in Serbian fourteenth-century architecture, especially in Churches founded by noblemen.
The façades were built in alternating layers of bricks and ashlars. Also, the façade walls of the church are decorated with blind arches that rest on lesenes.
As supposed by researchers the Church was built by Byzantine master builders (influence came from the nearby Thessaloniki like the Church of Saint Panteleimon, the small Church of the Holy Saviour and the Church of the Panagia Elassona Olympiotissa in Elassona).
The building was fresco decorated in the 14th century (after 1321) by Michael Astrapas, the famous Thessalonian painter of the Palaiologan era, and his associates .
The Church had a parakklesion once situated in the Eastern section of the South wall and was dedicated to St. John the Baptist, and was fresco painted in the 16th century. It was a single nave edifice with the width greater than the length and it was demolished in 1928.