Kobayr's main church was built in 1171, by Mariam, daughter of Kyurik II. At this time the Seljuks ruled Armenia, but delegated control to local princes. In 1195 and 1202, the Georgians defeated the Seljuk and gained control of the area. The Zakarian family, who adhered to the Georgian Orthodox Church) ruled the region. The Georgian Orthodox Church differed from the Armenian church in having accepted the views of the council of Chaldeon (451) over the duality of Christ's nature. This explains the occurrence of Georgian-styled frescos and inscriptions. Much of the south side of the complex has collapsed into the gorge deep below, leaving the apse exposed to the elements.