According to the most likely version of events, it was deserted at one point due to pirates causing problems to coastal hamlets and, like many other Cretan monasteries, it was renovated before 1600. The Church of Agios Georgios, the Catholicon of the Monastery, a cruciform domed basilica, was inaugurated during the late 16th century.
The great earthquake of 1856 destroyed a large part of the monastery and a decade later, the monks donated its property for the war of liberation of 1866. During the final Cretan revolution (1897-1898), Arsani suffered its own holocaust, with the Abbot Gabriel Klados meeting his doom after conflict with the Ottomans. This was the final contribution of the monastery shortly before the liberation of Crete.
The next landmark in the history of the monastery came in 1941, when the Germans executed monk Damianos Kallergis for fostering guerillas.
The monastery was renovated in the early 1970s, with the addition of murals to the church and the construction of the museum and conference center.
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