In the Ecclesiastical Museum are gathered many ecclesiastical relics of Nisyros which come mainly from the Monastery of  Panagia Spiliani  and its Parish  Panagia Potamitissa.

The museum consists of two main areas with exhibits of exceptional interest. It has plenty of material that includes from old candles, chalice, incense and church utensils, to old Gospels of the early 19th century, reliquaries, crosses, vestments and old seals.

It also has a large collection of coins and banknotes from the obol of the faithful, Greek and foreign, as well as various tributes and vows mainly to Panagia Spiliani.

Other items that have been collected and exhibited in the Ecclesiastical Museum of Nisyros are related to the ecclesiastical sacraments, such as old swimming pools, bridal and Nisyrian bridal ornaments or bridal jugs that brides used to wash before the sacrament. Also presented are various items related to the festival of Panagia Spiliani, such as old cauldrons that cooked revithada and clay dishes in which it was served to the world.

In addition, the museum houses a collection of 19th and early 20th century icons and a copy of  marble iconostasis  that Panagia Spiliani used to have.