In 1458 the Ottomans captured Attica. According to the French doctor Jacob Spon (1675), the sultan Mehmed II went to the Kaisariani monastery and there he was given the key of the city.
In 1678 patriarch Dionysius IV declared the monastery stavropegic, that is, independent of the archbishopric. In 1792 patriarch Neophytus VII revoked the privileges and the monastery again came under the Archbishopric of Athens.
The frescoes of the katholikon were painted in 1682 by Ioannis Ypatos, from the Peloponnese, sponsored by the wealthy Benizelos family, according to the inscription on the west wall. The narthex and most of the buildings of the monastery also date from the Ottoman period.
In 1745 a Russian pilgrim, Barsky, drew the monastery and its buildings. The drawing survives.
The monastery was also a place of learning. Greek Wikipedia says it hosted Theophanes in 1566 and Ioannis Dorianos in 1675, and that Theofanis Kavallaris taught grammar and sciences there from 1722 to 1728. It also says its library was famous. For the fate of the manuscripts the article gives accounts without documentation, so we do not repeat them here.