It is claimed that the monastery was home to her findings which included a piece of the Holy Cross from Jerusalem, the Cross of the Good Thief, a small part of the robe with which Jesus Christ was bound to the Cross with and a nail. This makes Stavrovouni Monastery a significant pilgrimage site in Cyprus.
Subsequent to its establishment, the monastery was occupied by Orthodox monks who lived under the rule of St. Basil; the Greek bishop of Caesarea Mazaca in Cappadocia.
As a result of several disturbances such as foreign invasions, poverty and the great fire of 1888, a lot of the antique that St. Helen found were lost. However, the True Cross remained untouched.
Having been under the rule of the Turks, there was a time in Cyprus between the 16th and 19th century where the monastery had no monks as said in historic documents. However, towards the end of the 19th century, monks slowly made a reappearance to revive the monastery. By the middle of the 20th century, the monastery was strong enough that it had sufficient monks to send some of them to other monasteries that needed recovering such as Panagia Trooditissa Monastery and the Monastery of Saint John the Baptist in Limassol.