Perched on one of the easternmost spurs of the Greater Caucasus crest, the monastery is part of the larger historic site of Nekresi, once a flourishing town of the Late Antiquity.

In medieval Georgian literary tradition, beginnings of monasticism at Nekresi is associated with the 6th-century monk Abibos, known for Christian proselytizing and combating Zoroastrianism.

That period saw an upsurge in monasticism in eastern Georgia, popularized by the Thirteen Assyrian Fathers, a group of monks who are credited by the medieval Georgian literary tradition with founding several monasteries across the country.

One of these men, St. Abibos, based at Nekresi, preached Christianity among the mountaineers east of the Aragvi and fought Zoroastrian influences—on one occasion quenching a sacred flame with water—until being captured and put to death.

The establishment saw its defensive structures fortified during the relatively stable reigns of successive kings of Kakheti, Leon (r. 1518–1574) and Alexander II (r.

[2] Subsequent turmoils and incessant marauding raids from the neighboring tribes of Dagestan compelled the bishop to transfer his see from the monastery to the relative security of the church of the Mother of God in the nearby village of Shilda in 1785.

Both were restored in modern Georgia after the fall of the Soviet Union: the former bishopric was reconstituted as the Eparchy of Nekresi within the Georgian Orthodox Church in 1995 and the monastery became repopulated by monks in 2000.

A long-established belief that it was a proto-basilica built on the place of a former Zoroastrian temple in the late 4th century—and, thus, one of the oldest Christian churches in Georgia—was disproved the 2008–2009 archaeological study which found no evidence of pre-Christian occupation at the site and redated the structure to the 6th century.

It belongs to a type of church building known in Georgia as a three-church basilica, in which the central nave and two side aisles are separated by solid walls.

Built of rubble with the additional use of limestone slabs, it is a centrally-planned church, with transitional features of a domed three-church basilica.

The ground floor is almost completely occupied by a wine cellar, with a large rectangular stone winepress in its northern part and a number of wine-jars (kvevri) buried underground.