The building operated as a nunnery (Monasterio Greco Madonna Acrotiriani) during the Venetian Era (17th century) and was a dependency of the monastery of Panagia Akrotiriani Toplou by Sitia. A document of 1671 states that the main temple was dedicated to St. John the Theologian, while there was another church dedicated to St. Peter.
After the conquest of Crete by the Turks, Tournatzis Basis Ahmet Aga turned the monastery into barracks of the local Janissaries. Healso built a small mosque and Ottoman baths. Later, the venue housed a Turkish orphanage.
After the liberation of Crete by the Turks, the place was used as a tobacco factory (Crete produced large quantities of smoke as the beginning of the 20th century). At the same time, the present church and the primary school of Agia Triada (Holy Trinity) were built.