Deposed by his former ward, he was forced to retire to a monastery under the name Joasaph Christodoulos (Greek: Ἰωάσαφ Χριστόδουλος) and spent the remainder of his life as a monk and historian.

[3] His close friendship with the late emperor and power over his successor had aroused the jealousy of his former protégés, Patriarch John XIV of Constantinople and Alexios Apokaukos;[citation needed] after a series of failed attempts, they succeeded in overthrowing his regency in September 1341 while he was out of the capital readying an army against the Crusader principalities that still held parts of the Peloponnesus.

[9] He accepted this, while continuing to style himself as the junior ruler to John V. The ensuing civil war lasted six years; calling in foreign allies and mercenaries of every description, the two sides completely disrupted and almost ruined the empire.

Apokaukos anticipated this move and sent a fleet to reinforce the city, obliging John to flee to Serbia, where Stefan Dušan sheltered him and lent him military support.

This proved largely ineffectual, and only the intervention of John's old friend and ally Umur of Aydin broke the regency's siege of his headquarters at Didymoteichon.

John VI attempted to rebuild the shattered Byzantine navy in preparation for the war he expected to follow a reduction of Constantinople's own customs dues.

[citation needed] In 1351, Kantakouzenos oversaw the Fifth Council of Constantinople, wherein Gregory Palamas' mystical hesychastic theology was declared Orthodox over the objections of Barlaam of Calabria and other Byzantine philosophers.

[3] He made his son Matthew Kantakouzenos another co-emperor in 1353,[13] but John VI's attempts to expand taxation to repay the government's debts had long been displeasing.

[3] By his wife Irene Asanina, a daughter of Andronikos Asen (son of Ivan Asen III of Bulgaria by Irene Palaiologina, Empress of Bulgaria, herself daughter of Michael VIII Palaiologos), John VI Kantakouzenos had six children: Kantakouzenos's four-volume History was published by Johannes Isacius Pontanus in 1603, by Ludwig Schopen at Bonn as part of the Corpus Scriptorum Historiae Byzantinae c. 1830, and by Jacques Paul Migne at Paris.

[17] He also wrote a commentary on the first five books of Aristotle's Ethics and several controversial theological treatises, including a defense of Hesychasm and a work Against Mohammedanism printed in Migne.