During the period of Venetian rule the Monastery of Chrysopigi developed into an important spiritual centre for Chania with numerous monks and a rich library.
In 1654, during the period of Ottoman rule, the Monastery became a Patriarchal Stavropegic establishment. It suffered greatly at Ottoman hands, sharing the fate of the rest of Crete. In 1821, on the outbreak of the Greek Revolution, it was destroyed and abandoned. In the years following 1848, however, the Monastery was renovated and rejuvenated with the advent of new monks.