The church was initially dedicated to the Virgin Mary. The name Anchiskhati was given to the church in the late 17th century, when the icon of the saviour was moved to Tbilisi from the Ancha Monastery in Klarjeti (now located in Turkey). The church was damaged and rebuilt several times from the 15th through the 17th century, due to wars with Persions and Turks.
In the end of 19th century the dome was added to the church, which significantly changed it. During the Soviet regime, the liturgical ceremonies in Anchiskhati church were halted, and it was turned into the museum of handcrafts, and later, into an art studio. The liturgical ceremonies were restored in the church in 1989.