This early part of the monastery's history ended approximately during the first half of the 13th century when the monastery was deserted due to constant pirate raids as well as due to the tremendous impact caused by the Fourth Crusade to the whole of the Byzantine Empire. The deserted monastery came initially under the jurisdiction of the Protos and later under the jurisdiction of Koutloumousiou monastery and later Philotheou monastery and functioned as a skete. In 1533, The monks of Philotheou sold Stavronikita to the abbot of a Thesprotian monastery, Gregorios Giromeriatis (Greek: Γρηγόριος Γηρομερειάτης). In 1536, a patriarchical edict by Patriarch Jeremias I reinstated Stavronikita's status as one of the monasteries of Athos, bringing their total number to 20. Therefore, Stavronikita became the last officially consecrated monastery of Athos and is usually referred as the last monastery to be added to the athonite hierarchy.