The close cultural interaction and coexistence in Anatolia was disrupted during the ten years of war starting with the Balkan Wars up until the end of the Greco-Turkish War. The change in attitudes came towards the Christian population, who were stigmatized as the “enemy within”. Different measures were applied in different regions for different communities all ultimately aimed at the same goal: the “cancerous element on the body of the sick man” needed to be removed. For example, unlike the Aegean Greeks who were subjected to religious conversion, the Turkish-speaking Orthodox Christians of Anatolia were tried to be homogenized with a “Turkish Church”. Despite not being supported by the ‘external power’ (Greece), they were still seen as unacceptable for the security of the state as long as they belonged to the Greek Orthodox Church. With a Turkish Church, their connection with the Patriarchate would have been broken and so they would have been tolerated. It was a non-violent Turkification method for the Turkish state to separate them from the sphere of the Greek Orthodox Church rather than assimilating them into Turksihness. On the other hand, for the Turkish-speaking Orthodox Christians, who did not have any faith in a return to peaceful coexistence in Anatolia, it was ‘abandonment of faith’ to avoid deportation by finding a modus vivendi with the Turkish authorities. In other words, the Turkish Orthodox Church was an attempt to accommodate the Turkish-speaking Orthodox Christians as an alternative to elimination. In fact, other methods were also tried, for example, the Ankara government asked the Vatican for the mass conversion of the Turkish-speaking Orthodox Christians to Catholicism. This paper investigates the case of the Turkish Orthodox Church by framing it in the homogenization policies of Turkey in the early 20th century in the light of British and Ottoman archival sources and with an analysis of the newspapers of the period.