Tamar in the Church of the Dormition, with a model of the church; an aetiological myth has the young Tamar, when out hunting with Giorgi, lost in the caves; when called for, she replied "I am here, uncle" (Georgian: აქ ვარ ძია) "ak var dzia", giving the site its name[1]

Soviet-era excavations have shown that the area of Vardzia was inhabited during the Bronze Age and indicated the reach of Trialeti culture. Cave settlements such as Uplistsikhe are known along the Kura River from at least the fifth century BC, while rock cut architecture in the context of Georgian Christianity is known from Zedazeni and Garedzhi from the sixth century AD, and more locally from Vanis Kvabebi, Cholta and Margastani from the eighth century.[1] Four distinct building phases have been identified at Vardzia: the first during the reign of Giorgi III (1156–1184), when the site was laid out and the first cave dwellings excavated; the second between his death and the marriage of his successor Tamar in 1186, when the Church of the Dormition was carved out and decorated; the third from that date until the Battle of Basian c.1203, during which time many more dwellings as well as the defences, water supply, and irrigation network were constructed; while the fourth was a period of partial rebuilding after heavy damage in the earthquake of 1283.[1]

A number of documentary sources supplement the knowledge derived from the site's physical fabric. The collection of chronicles known as the History of Georgia refers to Tamar erecting a church to house the icon of the Virgin of Vardzia after receiving divine help in her campaigns, before transferring the monastery from Upper or Zeda Vardzia. Tamar is said to have departed from Vardzia during her campaign against the Muslims, and her ensuing victory at Basian is celebrated in the Hymns in Honour of the Virgin of Vardzia by Ioane Shavteli. The History of Georgia also relates how Vardzia escaped the Mongol invaders in the 1290s. The monastery, according to chronicles, contained large amount of valuables from silver, gold and precious stones, indicating its economic prosperity. Construction on the site continued also after Tamar's death. The belltower and the southern church portal were built in the late 13th and early 14th centuries.

According to the inscription above the portal, the dining hall was constructed during the rule of atabeg Ivane, in the first half of the 15th century. Certain caves of the Ananauri complex were also built in the 15th and 16th centuries. The Persian Safavid chronicler Hasan Beg Rumlu describes Vardzia as a "wonder", "impregnable as the wall of Alexander the Great", before recounting its sack by the Persians under Shah Tahmasp I in 1551; a near-contemporary note in the Vardzia Gospel tells of its repatriation from a Persian bazaar. After the arrival of the Ottomans in 1578, the monks departed and the site was abandoned.[1] Part of the valuables were moved to the Imeretian village of Vardzia, where they were presumably used for construction of the church and the belltower.[2]