Mehmed II visited Athens after its surrender in 1458. Impressed by its monuments, particularly Akropolis, he granted Athens privileges. The town started to develop again after its Frankish decline. Daphni was returned to Orthodox monks, but the majority left the place due to the many piratical and bandit raids in the 16th and 17th century. On the other hand, Daphni was not completely deserted in the 17th and 18th centuries. Inscriptions and other written sources mention several abbots. Several archbishops visited the monastery too. D. Kampouroglou attributes the picture of abandonement to the attitude of the monks to avoid visitors. Nonetheless, the monastery emptied significantly in the 19th century, since it is rarely mentioned by historical sources.
During the first years of the 19th century, the notorious Lord Elgin (1766-1841) visited Daphni and according to various travellers removed three ionic columns from the façade of the exonarthex. They probably belonged to
the sanctuary of Daphnaios Apollon and are today in the British Museum.