He aided the Greek campaign in Smyrna in 1919 and was subsequently killed by a lynch mob after Turkish troops occupied the city at the end of the Greco-Turkish War of 1919–1922.

He studied at the Theological School of Halki starting at the age of 17,[3] and after graduating served as Archdeacon to Konstantinos Valiadis, the then Metropolitan of Mytilene.

When the Hellenic Army occupied Smyrna in 1919, at the beginning of the Greco-Turkish war, Kalafatis was reinstated to his office as metropolitan bishop.

Chrysostomos was on bad terms with High Commissioner Stergiadis (appointed by the Greek Prime Minister Venizelos in 1919) due to the latter's strict stance against discrimination and abuse in dealing with the local Turks, and his opposition to inflammatory nationalist rhetoric used in sermons, which he perceived as too political.

[4][5] US diplomat George Horton described how Stergiadis interrupted an important service at the Orthodox Cathedral in Smyrna:[6]Archbishop Chrysostom (he who was later murdered by the Turks) began to introduce some politics into his sermon, a thing which he was extremely prone to do.

[7] Chrysostomos wrote to (no longer Prime Minister) Eleftherios Venizelos in 1922, as Turkish troops were approaching, and shortly before the Great Fire of Smyrna, warning that "Hellenism in Asia Minor, the Greek State and the entire Greek Nation are descending now into Hell," and partially blaming him for his appointment of Stergiadis, "an utterly deranged egotist", even though he was an ardent supporter of Venizelos.

[8] After the defeat and retreat of the Hellenic Army in August 1922, Chrysostomos denied the offer to leave the city and decided to stay.

[11] Fahrettin Altay who witnessed the entry of the Metropolitan and the lynching mentions in his memoirs that religious leaders of the various millets were coming to congratulate the "Gazi".

The captain told him that Brigadier General Süleyman Fethi under the threat of bayonets did not say "Zito Venizelos" and had his blood spilled.

He adds that the metropolitan's black staff with an ivory, Byzantine Eagle symbolled head, which he had given to the soldier at the door of the building upon his entry, disappeared.