The initial temple of Agios Nikolaos (Saint Nicholas) was built inside the castle of Skaros and belonged to the Gyzi family. In 1651, the day of the celebration, it had been decided to transform the temple into a feminine monastery which by that time did not exist on the island. In 1674 it became Patriarchal- Stavropegic. Nuns settled in the building and the monastery operated normally until 1815. The nuns abandoned it after the departure of the last residents from Skaros.
The new monastery was founded in 1816 at the present day's spot between Imerovigli and Firostefani after the Patriarch had given the permission. Its catholic was a triunity. One chapel was dedicated to Agios (St) Panteleimonas and the other to Zoodochos Pigi. The central of St Nicholas was decorated with a wooden screen, a donation of the Gyzi family. The nuns took care of the transportation of pictures and ecclesiastical objects from the old monastery to the new one.
In 1834 when a royal decree shut down private monasteries and those with less than 6 monks and their possessions were taken by the state, the monastery of Saint Nicholas having 18 nuns was not shut down, remaining the only feminine monastery in the Aegean. During that period even 40 cells were not enough to house the increasing number of nuns, who still used to weave cotton fabrics as they did in the old monastery of Skaros.
In 1849 it ceased to be private but remained in good condition. In 1888 it housed 6 nuns.
In the 1956 earthquake it sustained some minor damage.
32 cells that were maintained in recent years are built in a square shape of a Festivities take place on the Agios Nikolaos, Agios Panteleimonas and Zoodochos Pigi days.