His eunuch Chrysaphius attempted to extort a present of gold to the Emperor but as he was unsuccessful, he began to plot against the new archbishop by supporting the archimandrite Eutyches in his dispute with Flavian.

The speech of Flavian remains, concluding with this appeal to the bishop of Dorylaeum: "Let your reverence condescend to visit him and argue with him about the true faith, and if he shall be found in very truth to err, then he shall be called to our holy assembly and shall answer for himself".

The Emperor Theodosius II, already angered by Flavian's refusal to pay him the customary bribe, was persuaded by the eunuch Chrysaphius to convoke another Council to Ephesus.

At this council, which assembled on 8 August 449, Eutyches was declared an orthodox teacher and reinstated, while Flavian was anathematised, deposed, and ordered into exile.

[6] The exact circumstances of Flavian's death, and the extent of Dioscorus' personal responsibility for it, are unclear and remain highly controversial in Eastern-Oriental Orthodox dialogue.

One deacon, Ischyrion, accused Dioscorus of ordering his syncelli (personal clerics) to murder people at Ephesus and even promoting them for the killings.

However, Richard Price and Michael Gaddis question the impartiality of these accounts, noting that these bishops had to place all blame for Flavian's death on Dioscorus to exculpate themselves.