The history of the monastery dates back to stylite practices in the 6th century and is linked by historical tradition with St. Anton, one of the Thirteen Assyrian Fathers.

[2] The foundation of the Martkopi monastery is associated in medieval Georgian tradition—elaborated in the hymns by the 13th-century cleric Arsen Bulmaisimisdze—with the monk Anton who is said to have arrived in Georgia from Edessa in Upper Mesopotamia around 545.

[4] In 1752, wary of the marauding Lesgian inroads, the bishop Ioseb Jandierishvili felt compelled to abandon the monastery and transfer his residence and parish within the better protected village of Martkopi.

In the process old Georgian murals and multilingual inscriptions were lost; a chamber discovered in the northern portion of the church was identified as the burial ground of St.

[2] On 26 August 1918, the Martkopi convent became the scene of the murder of Kyrion II, Catholicos-Patriarch of All Georgia, who was found shot in his own cell in unclear circumstances.

The monastery remained active until 1934, when it was closed down by the Soviet authorities; the church building was converted into an orphanage and later into a recreational facility for the Tbilisi-based 31st Aviation Factory employees.