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The cathedral was consecrated in 1362/3 by the Patriarch Kallisto I, who also designated the Monastery as the Patriarchial Seat. During this period, the frescoes were created by a leading Byzantine artist, whose name has unfortunately not survived. Two portable icons of Christ Pantocratoras also date from this same period, one of which is in the sacristy of the Monastery, and the other in the Hermitage Museum in St Petersburg. In the border of the latter, at the lower right, the figure of the founder Ioannis the Primikerios is still preserved. The founders endowed the Monastery with many other works of art, objects and relics, some of which are still safeguarded with special care in the Monastery today.

The dedication of the Monastery to the Transfiguration (Μεταμόρφωση) of Christ the Saviour has special meaning within the historical context in which it occurred. At that time in particular, Mt Athos strictly followed the ascetic system of hesychasm, or silent prayer. St Grigorios Palamas (who died in 1359), the most important defender of hesychasm, attached great significance to the event of the Transfiguration on Mt Tabor, where Christ revealed his divine nature to a select group of disciples. The goal of a hesychastic life is the union of man with the Holy Trinity, i.e., a union with the divine essence, the divine light and beauty of Christ, as witnessed by his disciples during the Transfiguration. (See also the surprising history of the Monastery’s artwork below.)

In the Will written by Ioannis in 1384, he states the following:
'Many years ago, while my late brother the renowned Commander of the Army was still alive, we built a Monastery together at the illustrious and brilliant Mt Athos, and we dedicated it to Christ the Almighty. Since he left this life, I have assumed the responsibility for the completion of the remaining work and, after having acquired for the Monastery many beautiful pieces of land and buildings in different areas as well as on Mt Athos, I continue to work even until now, albeit exclusively at my own expense, as much as my desire and my abilities permit…'
It is likely that he died prior to May 1387, and he was buried in the Monastery, next to his brother.

The Monastery of Pantokratoros (‘Christ, the Almighty Ruler’) was founded by two brothers, both high-ranking officers of Byzantium, at the difficult time when the Empire was in a state of decline. Alexis held the title of Great Primikerios (Μέγας Πριμικήριος; the 11th level of authority in the imperial hierarchy), and Ioannis held the title of Πρωτοσέβαστος (‘The First Respected’) in honour of his conquest of the Serbs in the lower valley of the Strymona River including Chrysoupolis, and his annexation of 15 kilometres of coastline west of today’s Kabalas from the Ottomans of Anaktoropolis, thereby also securing the island of Thasos.
In March 1357, the Emperor Ioannis V granted the brothers’ request: He transferred the administration of the areas they had conquered to them, including the taxes derived from them, which in effect marked the beginning of the founding of the Monastery. Between April and June of the same year, both brothers were promoted by the Emperor: Alexios to the position of Commander of the Military (μέγας στρατοπεδάρχης), while Ioannis was awarded the former rank of his brother and became Great Primikerios. The local inhabitants referred to the brothers as ‘our own true saints’.
Alexis, who was probably unmarried, died between March 1368 and February 1369, and was buried on the grounds of the Monastery. Ioannis, who was married to Anna Asanina, a close relative of the Emperor, continued to support the Monastery on his own and in 1384, obviously after the death of his wife, he took up residence there as a monk.