The monastery was at first under the jurisdiction of the Jerusalem patriarch; its independence was recognized by Constantinople in 1575. The number of monks is limited to 36; this figure includes those living in annexes (metochia) elsewhere, which today are chiefly at and Suez in . The laity of the Church of Sinai are some Christian Arabs employed by the monastery and fishermen on the coast at al-Ṭūr (Tor, formerly Raithu). The Muslim Bedouin Arabs who live near the monastery have always acted as its guards and have in turn been supported by it.
Founded in 527 by the emperor , the building of the monastery dates from 530 CE, when Justinian, after complaints of robber incursions from the hermit monks who had settled there, fortified the traditional site of the observed by on the lower slopes of Mount Sinai. During the 7th century the monastery provided a centre of refuge for scattered of Christians threatened by the rise of . Spared by the Muslims, the monks, according to tradition, conciliated the invaders by erecting the small within the walls where local Bedouin Arabs still worship. The monastery was a centre during the Middle Ages. St. Catherine’s still retains much of its original appearance and has had an unbroken history since the 6th century. The original gray granite walls (280 by 250 feet [85 by 76 metres]) still stand, and so does the church dedicated to the Virgin Mary, which was built at the same time. In the apse is a restored of the Transfiguration, also dating from the early Byzantine period.