On November 9, the monastery's defences were breached. Giaboudakis was ordered by Abbot Gabriel Marinakis to blow up the gunpowder room where the elderly, women and children had taken refuge. Giaboudakis announced his intentions and asked if anyone preferred to leave the room and take their chances. He then waited until the Turkish troops started pounding the room's door and blasted the gunpowder causing the explosion that took the lives of all the Greeks present and several hundred Turks.
Though it is generally accepted that Giaboudakis blew up the gunpowder room, some claim that Emmanouil Skoulas was the man who actually pulled the trigger.