The Bolnisi Sioni church is the only remaining three aisled basilicas in Georgia. It was constructed using carved stones, with its primary layer being different from the layer of bricks and river stones. The temple is decorated with clear green-turquoise hued stones. Decorations of the bases and heads of the pillars are of particular interest; one of them is known as the Bolnisi Cross. This is also the first known monument of Georgian architecture that utilizes relief sculptures related to the pre-Christian period, but adopted by the Christian era as well (ex: the head of a bull, various birds and animals).

In 1936-39 wide-scale architectural and restoration works were conducted in Bolnisi. The monument was fully cleaned, fixed and fortified. During this period architects discovered a stone with scripts at one of the entrances. All three scripts of Bolnisi Sioni are ancient examples of Georgian writing and language. One of the scripts, belonging to the 5th century, is located on the eastern wall above the window of the altar. This script is now preserved in the State Museum, while the temple has a replica of the original. King Peroz of Iran ruled over the region containing Bolnisi Sioni in 459-484, meanwhile the construction of the church started in 479 and was finished in 493. Frescos of the Mother of God and Jesus Christ are above the window. Both of these icons have been damaged. According to local legend, during the Soviet period, people were taken to the church and tested their belief of God: they had to shoot the icons as proof of their atheism. The icon of the Mother of God, which has been said to perform miracles, is located on the right side of the altar. There are violets that blossom behind the chamber of monks all year round, where 500 inhabitants of Bolnisi were tortured in the 17th century. Currently Sioni is an active church.