It has existed from at least the 9th century, and has numbered among its monks many important figures in Georgian ecclesiastical history. At the end of the 13th century Sapara became a possession of the Jakeli family, whose leader, Sargis Jakeli, was adept at staying on good terms with the Mongols, which enabled Samtskhe to enjoy a peace unusual for the time. When he grew old, Sargis took monastic orders and changed his name to Saba. His son Beka built the largest of the 12 churches here, St Saba's Church, named after the saint whose name his father had adopted, one of the most architecturally important churches of its time. The 14th-century frescoes inside are of high quality.
From the end of the 16th century until the beginning of the 17th century the Sapara Monastery became empty due to the expansion of Turkish policy into Samtskhe and during this process the monastery's icons and other treasures were taken to more protected areas of Georgia.