[1] It is built on a lush green location at an altitude of 538 meters, approximately 24 km east of Heraklion.

According to tradition, it received its name from a Jerusalem sage bush (agarathia in the Cretan dialect), under which an old icon of Virgin Mary was found.

During the Ottoman occupation of Crete, the monastery often served as a local revolutionary center and suffered several retaliatory attacks as a result.

Several important figures, among which Cyril Lucaris, Meletius Pegas,[3] Joseph Bryennios, Gerasimos Palaiokapas and Theodore of Alexandria, have been enrolled as monks at Agarathos.

The main building (katholikon) is a two-nave church that was erected on the location of an older one and was inaugurated in 1894.