By the mid-1800s, the Turks had occupied Crete for more than two centuries, despite frequent bloody uprisings by Cretan rebels, including the Daskaloyiannis Revolt of 1770 and their participation in the Greek War of Independence of 1821. In the 1866 rebellion, the monastery became the rebels' headquarters, owing to its central position on the island and it's strategic location.
There were 259 rebels in the monastery and 12 out of the 16 revolutionary committee's members. In addition to the rebels and revolutionary leaders, there were 700 unarmed women and children from nearby villages who were seeking refuge from the Turks.
On November 8, 1866, the Monastery was surrounded by 15,000 Turkish soldiers under Suleyman Bey, armed with 30 cannons. The Turkish commander gave Abott Gabriel Marinakis an ultimatum, which was to either surrender or the Monastery would be destroyed. The ultimatum was answered by gunfire from the rebels.
The following day, the Turks by sheer weight of numbers penetrated the Monastery's walls. As they poured into the inner courtyard, they fought hand to hand with the rebels. The women and children sought refuge in a gunpowder room where they decided it would be better to blow the monastery up than surrender to the Turks. Konstantinos Giaboudakis set the gunpowder off and caused the explosion which killed the besieged Greeks and several hundred Turkish soldiers.
864 Greeks were killed in the battle for Arkadi as were over 1,500 Turks and Egyptians .