Everything indicates that the cave has been inhabited by hermits since Byzantine times, but during the 16th century the area was exposed to pirate attacks and the monastery was destroyed. Even though the locals quickly repaired the worst damages, another couple of centuries would pass, until the area began to flourish again. This happened in 1841 when Gerontogiannis took possession of the monastery from its then owner Chatzis Nikolaos Zafeiris.
Gerontogiannis started to repair and extend the few buildings of the monastery, but the work did not make much progress because of his many church duties. His stay on the island of Kassos, near Karpathos, some years later delayed his work even further.
Not till after 1861 the work speeded up. Monk's cells, rooms for pilgrims, kitchens and cisterns were built, but primarily, the church was extended into two naves of which the inner (and oldest) is dedicated to St John the Baptist, while the new one is dedicated to the Holy Trinity.
The wood carver Chatzis Minas from Lassithi made in 1869 the beautiful templo (the picture-wall between the nave and the choir of the church) for which the saint-painter Antonios Alexandridis painted icons the following year.
After Gerontogiannis' death in 1874, most of the monks left and the monastery was allowed to fall into decay, until his grandson, Iosif Gerontakis, was made the abbot of the monastery some years later. Iosif was - as his grandfather - very dynamic and he extended the monastery with new monk's cells, cultivated the land around the monastery, brought a water pipe to the monastery from the spring at the nearby Agii Saranta church, and he furthermore extended the Panagia monastery in the nearby little village of Kalo Nero.
The Kapsa monastery worked independently until the year 1900 when it, owing to a shortage of monks, was placed under the Toplou monastery, which is still sending an ordained monk to Kapsa to read mass and to inspect the monastery that meanwhile has become a convent.
From the western part of the monastery's back side a flight of steps leads up to the cave where Gerontogiannis lived as a hermit. The cave is situated on the steep slope of the Pervolakia gorge and has a beautiful view over the area and the Libyan Sea.