It is assumed that the church building was erected during the reign of the Byzantine Emperor Isaakios I Komnenos (1057-1059). The existence of the Church Sveta Bogorodica Črьnogorska is beyond doubt attested from the 14th century. The monastery is mentioned in the boundary description of the village of Črěševo, which forms part of a donation by the Serbian King Stefan Uroš II Milutin (reigned 1282-1321) to the Monastery of Saint George-Gorg near Skopje (ta nad Svetuju Bogorodicu črьnogorьsku do Črьnoga kamene). The Vita of the Serbian Emperor Stefan Uroš V (reigned 1355-1371), written by the Serbian Patriarch Pajsije, reports that Stefan Uroš V and his mother Jelena completed the Church Sveta Bogorodica Črьnogorska after the death of the Serbian Emperor Stefan Uroš IV Dušan (reigned 1331-1355) (I togda blagočьstivaa carica sь sinomь svoimь sьvršajutь crьkovь ostavšuju ōt blagočьstivago i prěvisokago cara Stefana vь črьnoi gori ne sьvršena i trudomь i podvigomь i pomoštïju prečistye vladičice naše i bogorodice i svoihь praroditeь pomoštïju i zastupljenïemь sьvrьšajutь crkьvь prěslavnuju vь pohvalu i slavu uspenïe prěčityje i prěblagoslovenïe vladičice naše i bogorodice i prisnoděvy marie i do dьnьsь iměnuetse črьnogorska bogorodica). It is unclear, whether the Church of Sveta Bogorodica Črьnogorska is identical with the church in the Skopska Crna Gora above Žegligovo built by Jelena, the mother of Stefan Uroš V, which is attested in the Serbian genealogies (rodoslovi) and annals (letopisi) (u Črьmьnyje Gory, vyše Žegligova; eius vero mater aedificavit Ecclesiam in Nigro Monte, supra Segligovo). The Ottoman Sultan Murad I (reigned 1360-1389) might have passed by the Church Sveta Bogorodica Črьnogorska on his march against the Serbian Prince Lazar Hrebeljanović (reigned 1373-1389) before the battle on the Kosovo field (Kosovo Polje) in 1389. Evdokija Balšić commissioned the monk Gerasim in the Monastery of Sveta Bogorodica Črьnogorska in 1409 to write the manuscript of the Dialogues (paterik) by Saint Gregory the Great (...sia božestvennaja kniga, glagoljemaa dialogь, ispisa se iže vь ōbitěli prěčityje i prěslaьnyje vladyčice naše bogorodice nerukotvorennyje čjudotvorice črьnogorьskye povelěnïem blagověrnyje i blagočьstivyje i hristoljubivyje gospogje despotice kyr Eudokyje, dьšti blagověrnago i hristoljubivago i velikago gospodina Gjurgja Balšikja...). The scribe Vladislav Gramatik resided in the Monastery of Sveta Bogorodica Črьnogorska between 1457 and 1497. In 1479 he compiled a liturgical book (panegyrikon) in the Monastery at the foot of the Crna Gora in the region of Žegligovo (monastiri prěsvetyje vladičice naše bogorodice iže vъ podkrilïi Črьnye Gory, vь prědělě Žegligovʼcěm). The scribe Dimitrij Kantakuzin also temporarily resided in the monastery. The scribal notes of both copyists mention the Monastery of Sveta Bogorodica Črьnogorska in the year 1469 (vь vьsečьstněmь monastiri prěsvetye bogorodice suštee iže v podkrilïi Črьnye Gory), 1473 (vъ vъsečъstněm monastiri prěsvetye vladičice naše bogorodice i prisnoděvy Marïe, suštee iže v podkrilïi Črъnye Gory), 1479 (vь vьsečьstněm monastiri prěsvetyje vladičice naše bogorodice iže vъ podkrilïi Črьnye Gory, vь prědělě Žegligovʼcěm) and 1480/81 (Vladislavu dïaku ōt Črьnogorskye bogorodice). The Monastery of Sveta Bogorodica Črьnogorska is registered as "Holy Mother of God in Kara Donlu" or "Monastery Karadonlu with the second name Holy Mother of God" in the Defter for the Sanjak Köstendil from the years 1570 to 1572. In the 17th century (between 1647 and 1654) the Serbian Patriarch Gavrilo Rajić payed a visit to the Monastery of Sveta Bogorodica Črьnogorska (Da se zna kogda pridohь azь arhiepiskopь Gavriilь vъ carьnogorsku bogorodicu). The British traveller Edward Brown saw most probably the Monastery of Sveta Bogorodica Črьnogorska, when he passed through the city of Kumanovo in 1668/69 (near which [scil. Kumanovo] there is still a Greek Monastery, upon the side of the Hills).
The Church has a ground plan of an inscribed-cross with five domes, resembling those of Staro Nagoričine and Church of St. Panteleimon in Nerezi (near Skoplje), narthex and a three-partite apse. The central dome has a twelve-sided drum and is set on four massive pillars. The smaller domes, erected in the shape of octagons, are located in the corners of the building - the eastern ones are situated on the prosthesis and the deaconry, and the western ones above the narthex. The narthex is decorated with a modest architectural sculpture. The Church is vaulted with barrel and cruciform arches, placed on the walls, pillars and pilasters in the interior of the building. The façade is decorated with lesenes.
This Church is a true representative of the building traditions of the Palaiologan epoch, such as Churches in Arta, Mistra and Thessaloniki.
The Church has been fresco painted between 1348 and 1352, representing the largest painted ensemble on the Macedonian territory in the 14th century and the second largest in the Balkans.