The first monastery on the site dates to the 7th century, expanded in the 10th. Then came the Seljuks, whose wars with the Byzantine Empire in the 11th and 12th centuries damaged the complex severely. Recovery came from an unexpected quarter: when the Mongols of Hulagu Khan, grandson of Genghis Khan, conquered the region in the mid-13th century, they signed a peace agreement with the Armenian Church. Under the stability of the Ilkhanate, the monastery was restored. A complete rebuilding under the leadership of Zachariah in 1330 marked the beginning of Saint Stepanos's golden age. By the 14th and 15th centuries, the monastery had become a center of cultural and intellectual life, producing illuminated manuscripts in religion, history, and philosophy.

The Safavid dynasty initially protected the Armenians, but the region sat at the violent center of Ottoman-Safavid conflicts. When the Ottomans invaded Western Armenia in 1513, the monastery began a slow decline. Abbas the Great delivered the final blow in 1604, expelling the entire population and leaving the monastery abandoned. For nearly half a century it stood empty. After 1650, the Safavids reoccupied the region and restored the complex, giving it a second life. The Qajar rulers continued this protection, encouraging a major rebuilding between 1819 and 1825. By then, the Treaty of Turkmenchay had drawn a new border along the Araxes, splitting the Armenian world between Russian and Iranian spheres. The monastery found itself on the Iranian side, which may have preserved it from the destruction that befell Armenian sites across the river.

The monastery's architectural power comes from its setting as much as its construction. Canyon walls tower above the complex, which includes the main church, a bell tower, ancillary buildings, and ramparts. The dome's interior is decorated with detailed reliefs and painted scenes. Wall carvings depict biblical narratives with a craftsmanship that reflects centuries of Armenian artistic tradition. The exterior combines Armenian decorative motifs with influences absorbed from the various empires that passed through -- Persian, Mongol, Ottoman. Several restorations in the 20th century stabilized the structure without erasing its layered history. Today the monastery stands as one of the best-preserved examples of Armenian monastic architecture anywhere in the world, its survival made possible by its location on the Iranian side of a border that has separated communities for two centuries.