In the Ottoman period the church was converted into a mosque by Recep Aga, steward to Kiopruli, the conqueror of Chandax, who thus lent his name to the surrounding area.

The building was also known as the Sivri Cesme Mosque (mosque of the conical fountain), on account of a pointed drinking fountain that stood opposite it.

Following the liberation of Crete from Ottoman rule, the Church of St. Anastasia became "exchangeable estate" together with the majority of buildings, regardless of whether they were monuments.

The church was declared a listed building in 1947. To this day it is privately owned and is used as a shop.