The Ottomans, in retaliation for the spread the Greek Revolution, arrested him together with other hierarchs and imprisoned him for 7 months in the dungeons of a prison of Constantinople.

In 1822, after the hanging of Gregory V and the death of his successor Eugenius II of Constantinople from torture suffered at the hands of the Ottomans, Anthimus, who was still imprisoned, was elected Patriarch.

Anthimus III also refused to allow a British Protestant to publish a translation of the Bible to Demotic Greek by the Patriarchal typography.

[citation needed] In 1824, Anthimus III was deposed by Sultan Mahmud II because he refused to cooperate with him against the Greek Revolution, and with the accusation that he favoured the independence of the Serbs from the Ottoman Empire.

His magnificent funeral was held by the Metropolitan of Ephesus, Anthimus VI of Constantinople and was buried in the church of John the Theologian, where until the Asia Minor Catastrophe there was also a big icon of him.