When the Patriarch of Antioch claimed the Church of Cyprus was under its jurisdiction, the Cypriot clergy denounced this before the Council of Ephesus.

The church was thus able to send a cogent argument on its own behalf to the Emperor: the discovery of the relics of its reputed founder, Barnabas.

Zeno confirmed the status of the Church of Cyprus and granted its Archbishop the "three privileges": namely to sign his name in an ink made vermilion by the addition of cinnabar; to wear tyrian purple instead of black robes under his vestments; and to hold an imperial sceptre (i.e. a gilt staff of silver, topped by a gold globus cruciger) instead of the regular episcopal crosier.

Cyprus suffered greatly from Arab invasions in the following centuries, and during the reign of Justinian II the cities of Constantia, Kourion and Paphos were sacked.

After the establishment of the Kingdom of Cyprus, the Catholic kings gradually reduced the number of Orthodox bishops from 14 to 4 and forced those away from their towns.

The local Orthodox Christians shared some of the benefits of the economic development of Cyprus and especially Famagusta at the time.

[6] Churches containing Byzantine icons, frescoes and mosaics have been pillaged by antiquities dealers and sold on the black market.

One of the most prominent cases of pillage was of the mosaics of Panagia of Kanakaria of the 6th century AD, which were finally returned to the Church of Cyprus, following rulings by federal courts in Indianapolis and Chicago.

In old age, Archbishop Chrysostomos suffered from Alzheimer's disease and was unable to carry out his duties for a number of years.

In May 2006, Ecumenical Patriarch Bartholomew I chaired a broader meeting of church elders which called for Chrysostomos' "honorary removal".

The Holy Synod meets regularly in the first week after Easter and in the first fortnight of the months of February and September.