Being suspected by the empress Anna of Savoy and opposed by a powerful party at court (including Kantakouzenos' one-time protege Alexios Apokaukos), he rebelled, and had himself crowned emperor at Didymoteichos in Thrace, while John V Palaiologos and his supporters maintained themselves at Constantinople.
The civil war which ensued lasted six years, during which the rival parties called in the aid of the Serbians, Bulgarians, and the Ottoman Turks, and engaged mercenaries of every description. It was only by the aid of the Ottoman Turks, with whom he made a bargain, that John VI Kantakouzenos brought the war to an end favourable to himself.
In 1347, he entered Constantinople in triumph with an army of 1,000 men, and forced his opponents to an arrangement by which he became joint emperor with John V Palaiologos and sole administrator during the minority of his colleague.
He made his own son Matthew Kantakouzenos a co-emperor in 1353.
During this period, the empire, already broken up and reduced to narrow limits, was assailed on every side. There were wars with the Genoese, who had a colony at Galata and had money transactions with the court; and with the Serbians, who were at that time establishing an extensive empire on the north-western frontiers; and there was a hazardous alliance with the Turks, who made their first permanent settlement in Europe, at Gallipoli in Thrace, towards the end of his reign. In 1349, he sent a newly-built fleet of 9 fair-sized ships and about 100 smaller ones against the Genoese, but it is completely captured by the Genoese. Then in 1351, he sent 12 ships to help Venice against Genoa, but the fleet was defeated.
Kantakouzenos was far too ready to invoke the aid of foreigners in his European quarrels; and as he had no money to pay them, this gave them a ready pretext for seizing upon a European town. The financial burdens imposed by him had long been displeasing to his subjects, and a strong party had always favoured John V Palaiologos. Hence, when the latter entered Constantinople at the end of 1354, his success was easy.
Kantakouzenos retired to a monastery (where he assumed the name of Joasaph Christodoulos) and occupied himself in literary labours.
In 1367 Joasaph (as he was now known) was appointed the representative of the Eastern Orthodox Church to negotiate with Paul of Smyrna then the Latin Patriarch of Constantinople to attempt a reconciliation of the Eastern Orthodox and Roman Catholic Churches. They agreed to call a grand ecumenical council to be attended by the Pope, all the Patriarchs and bishops and archbishops of both the eastern and western churches. This plan was subsequently refused by Pope Urban V and so nothing came of it.