In Paul's tenure as patriarch, the Church suffered schisms, first with the tritheists, then with the Egyptian non-Chalcedonians after a failed attempt to consecrate a new pope of Alexandria, and finally with the eminent bishop Jacob Baradaeus, who in his effort to reunite the Egyptian and Syrian non-Chalcedonians agreed to Paul's deposition, dividing the Church in the process.
[9] In 565, at Theodosius' request, Paul travelled to Egypt, with John of Kellia, Leonidas, and Joseph of Metellis, to perform ordinations and manage other ecclesiastical matters in his stead.
[14] Paul came under criticism for his opposition to tritheism, and its proponents claimed he was opposed by Jacob Baradaeus and Theodore of Arabia, to which they responded by formally reaffirming their support for him.
[15] In 570,[16] the tritheists appealed to Emperor Justin, and he arranged for a disputation to be held under the auspices of the Chalcedonian Patriarch John Scholasticus of Constantinople.
[19] John Scholasticus invited Paul, who was residing at the monastery of the Acoemetae in Constantinople, and the bishops John of Ephesus, Stephen of Cyprus, and Elijah, to the patriarchal palace to discuss ending the schism, but upon their arrival there they were detained until they had agreed to subscribe to the Emperor Justin's edict, thus entering into communion with the Imperial Church.
[20][21] Paul was excommunicated by Jacob Baradaeus for accepting communion with the Imperial Church, and he remained in captivity until he managed to escape in 574, and fled to the encampment of the Ghassanid King Al-Mundhir III ibn al-Harith, and then to the Mareotis region in Egypt disguised as a soldier.
[6][21] Theodore made no effort to establish himself as pope of Alexandria and retired to his monastery, and Peter was accepted by the majority of the Egyptian non-Chalcedonians.
[30] In 577, the faction in favour of Theodore's papacy collapsed as Longinus went into exile in Arabia, whilst Paul went into hiding at Constantinople.
[33] A synod at Constantinople was held by Al-Mundhir in March 580 to heal the division between the Jacobites and Paulites, and at its conclusion, Damian agreed to end the schism with Paul.