The cemeteries serving the Muslim residents of Spinalonga are arranged on the island's eastern side, along the opposite shores, where the village of Plaka is located today, and on the Spinalonga peninsula.

The cemetery in the eastern part of the island, which is low and against the fortification wall, is known thanks to a photograph taken by Italian archaeologist Giuseppe Gerola during his visit to the fortress in 1901. In the photograph, the tombstones are visible, which, according to Muslim tradition, are placed in pairs on each grave; one is positioned at the head of the deceased, and the other at the feet. Many of these tombstones are later used as building materials during the period of the Leper Colony. Visitors can see some of them in the exhibition space of the Ottoman-era shops.