As mentioned on an inscription over the portal connecting the narthex to the main temple, inside the catholicon, the monastery was established in 1077, during the reign of emperor Michael VII Dukas (1071 – 1078), under the tenure of Ecumenical Patriarch Cosmas I of Constantinople (1075 – 1081). Its founder was St Arsenios of Varnakova, a monk from Karya (Doris), who dedicated the first temple to the Nativity of Virgin Mary. The monastery also celebrated the Assumption of the Virgin, which finally prevailed as its main feast day.
During the reign of Alexius I Comnenus (1081 – 1118) and under the tenure of Ecumenical Patriarch Nicholas III Grammaticus (1084 – 1111), the original temple, along with the monastery complex, was frescoed and completed. Later, in 1148, a second magnificent temple was established. Alexius Comnenus himself took his final vows and assumed the name Acacius, and he was buried in the Temple of Virgin Mary. Also buried in the same temple was Manuel I Comnenus (Porphyrogenitus), successor of John II Comnenus, who had succeeded Alexius I to the throne. During that period, the monastery possessed many glebes in the surrounding area, with some of which allotted by the Comnenus family. This is indicative of the monastery’s importance. In the early 13th century, 96 friars and deacons were recorded to live there, while the property of the monastery definitely matched its repute.
After the Sack of Constantinople in April 1204, the monastery was placed under the rule of the Despotate of Epirus (1204 – 1359) until the Despotate’s collapse in 1359, when it was placed under the restored Byzantine Empire.
It is said that the Palaiologus dynasty of the Byzantine Empire favoured the monastery just like the Comnenus dynasty had done in the past.
During that period, particularly when St David became the igumen (abbot) (1520 – 1532), the monastery prospered. At the beginning of the 16th century, a Hellenic school of lycée type operated until 1900. Central figure and a teacher at the school was the friar Nicodemus Kavasilas (1595 – 1652). In 1578, the monastery had about 200 friars, as the Prothonotary of the Patriarchate of Constantinople, Theodosius Zygomalas, informs us.
During the Ottoman occupation, the Monastery played a decisive role as a national and patriotic centre. It served as a hideout and as a base of operations of clephts and armatoles from the surrounding areas and from elsewhere. Some of them were Dimos Skaltsas/Skaltsodimos, Konstantaras or Zacharias, and Kalyvas. Because of that, there were many occasions when the monks became involved in armed conflicts with the Ottomans, as they were hiding persecuted Greek warlords. Additionally, an important figure in the battles that took place in the area during the Revolution was the monk Parthenius Zografos. His contribution to the struggle led people to call him “the Dorian Papaflessas”.
In the sixth year of the Revolution (1826), a few weeks after the Exodus of Messolonghi, Reşid Mehmed Pasha (Kütahı) with an army of 4000 soldiers, on his way east, laid siege to Varnakova, where Greeks that had survived the Fall of Messolonghi had taken shelter. At the time, Cosmas Theocharis was igumen of the monastery. Besides the monks and women and children, in the monastery were fortified many local and other chieftains (Kitsos Tzavelas, K. Kalyvas, Apokoritis). The siege lasted for days, but the Ottomans could not take the monastery. After repeated failed attempts at breaking the barricades around the monastery, they secretly decided to dig underground, so that they could blow the monastery up from underneath. However, their plan was betrayed to the monks by an Albanian man. Thus, on May 26 the fortified Greeks made their escape, with two monks and a countryman as casualties. Following the exodus, the monastery was blown up by the Ottomans. Five years later, in 1831, it was rebuilt by Ioannis Kapodistrias, who gave a grant – likely his own money – of 1,800 pfennigs. Kapodistrias is considered the second ktetor (donor) of the monastery.
After the establishment of the new Greek State, the monastery started operating again, albeit without the same property or size it used to have. In 1984, the monastery was deserted, and, from 1992 on, it has been converted into a female convent.