Michael was appointed patriarch by the Byzantine emperor Manuel I Komnenos, culminating what had been a highly distinguished intellectual and administrative career.

The most important of his appointments before receiving the Patriarchal throne was the office of hypatos ton philosophon (ὕπατος τῶν φιλοσόφων, "chief of the philosophers"), a title given to the head of the imperial University of Constantinople in the 11th–14th centuries.

Michael III also ordered a review of Eastern Orthodox ecclesiastical and imperial laws and decrees by Theodore Balsamon, Patriarch of Antioch, known as the "Scholia" (Greek: Σχόλια) (c. 1170).

[6] The ruling of the council was described by Macarius of Ancyra, Metropolis of Ancyra: "And when, after having said and heard many things, as chance would have it, they [the Latins] were for making no concessions, but insisted that everybody should give way to them unreservedly, and adopt their customs, all hope being gone, the emperor, the council, and the whole senate, gave their vote in favour of a total separation from the pope and those who thought with him, and referred it all to the judgment of God.

[7] Even if a pro-western Emperor such as Manuel I agreed to it, the Greek citizens of the Empire would have rejected outright any union of this sort, as they did almost three hundred years later when the Orthodox and Catholic churches were briefly united under the Pope.