In 1907, following Bulgarian complaints and Russian pressure, Karavangelis was removed from his position by orders of the Sultan. He returned to Constantinople as a Synod until the collapse of the Diocese of Amaseia in January 1908. The Patriarch had requested that Karavangelis fill the recently vacated position, and so he became the Metropolitan of Amaseia, based in Sampsounta. There, he helped create schools in the most remote villages and established a high school for Greek education. He also assisted in the formation of armed groups to defend the Greek and Armenian population from Turkish aggression and persecution by the Young Turks. During massacres of local Armenians, Karavangelis along with Chrysanthos of Trebizond and Bishop Efthymios were able to save hundreds by hiding them in the Metropolitan Church and other Greek homes. Their efforts were recognized by a United States based Armenian newspaper. For his actions, he was arrested and sent to Constantinople in 1917, where he would remain in prison for some time.