Kalafatis was born in Triglia in 1867, one of eight children born to Nikolaos and Kalliopi Lemonidos Kalafatis. He studied at the historical Theological School of Halki from the age of 17, and served as Archdeacon to Konstantinos Valiadis, the then Metropolitan of Mytilene. Kalafatis served as chancellor and in 1902 became the Metropolitan of Drama, a city in northeastern Greece. His vocal nationalism caused the Sublime Porte to request his removal in 1907, and he eventually returned temporarily to Triglia. In 1910 Kalafatis became the Metropolitan of Smyrna.
Smyrna
Kalafatis had not been in good terms with the Ottoman authorities and he was displaced in 1914. When the Greek 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 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. US diplomatGeorge Horton described how Stergiadis interrupted an important service at the Orthodox Cathedral in Smyrna:
Archbishop Chrysostom began to introduce some politics into his sermon, a thing which he was extremely prone to do. Stergiades, who was standing near him, interrupted, saying: "But I told you I didn’t want any of this."
Chrysostomos was an ardent supporter of the cause of Greek nationalism, while Stergiadis was seen by some as behaving in a perversely defeatist manner. Chrysostomos wrote to 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.
Lynching
After the defeat and retreat of the Greek army in August 1922, Chrysostomos denied the offer to leave the city and decided to stay. On 10 September 1922, soon after the Turkish army had moved into Smyrna, a Turkish officer and two soldiers took Chrysostomos from the office of the cathedral and delivered him to the Turkish commander-in-chief, Nureddin Pasha. The general decided to hand him over to a Turkish mob who murdered him. According to French soldiers who witnessed the lynching, but were under strict orders from their commanding officer not to intervene:
"The mob took possession of Metropolitan Chrysostom and carried him away... a little further on, in front of an Italian hairdresser named Ismail... they stopped and the Metropolitan was slipped into a white hairdresser's overall. They began to beat him with their fists and sticks and to spit on his face. They riddled him with stabs. They tore his beard off, they gouged his eyes out, they cut off his nose and ears."
Bishop Chrysostomos was then dragged into a backstreet of the Iki Cheshmeli district where he died soon after.
Family Survivors
Metropolitan Chrysostomos was survived by his nephews, among whom was Yannis Elefteriades, who witnessed the arrest and execution of his uncle, having found shelter by his side after the killing of his parents. He escaped as a refugee to Lebanon, where today his grandson Michel Elefteriades is a well-known Greek-Lebanese artist and producer.