Early in his patriarchate, Flavian angered a state official named Chrysaphius by refusing to offer a bribe to the emperor. The ruler's wife Eudocia joined the resulting conspiracy which Chrysaphius hatched against Flavian, a plot that would come to fruition in an illegitimate Church council and the patriarch's death.
As head of the Church in Constantinople, Flavian had inherited a theological controversy about the relationship between deity and humanity in the person of Jesus Christ. In an occurrence that was not uncommon for the time, the doctrinal issue became entangled with personal and political rivalries. Flavian's stand for orthodoxy gave his high-ranking court opponents a chance to act against him by encouraging the proponents of doctrinal error and manipulating the emperor in their favor.
The theological issue had arisen after the Council of Ephesus, which in 431 had confirmed the personal unity of Christ and condemned the error (known as Nestorianism) that said he was a composite being made up of a divine person and a human person. But questions persisted: Were Jesus' eternal divinity, and his assumed humanity, two distinct and complete natures fully united in one person? Or did the person of Christ have only one hybrid nature, made up in some manner of both humanity and divinity?
The Church would eventually confirm that the Lord's incarnation involved both a divine and a human nature at all times. When God took on a human nature at the incarnation, in the words of Pope St. Leo the Great, "the proper character of both natures was maintained and came together in a single person," and "each nature kept its proper character without loss."
During Flavian's patriarchate, however, the doctrine of Christ's two natures had not been fully and explicitly defined. Thus, controversy came up regarding the doctrine of a monk named Eutyches, who insisted that Christ had only "one nature." Flavian understood the "monophysite" doctrine as contrary to faith in Christ's full humanity, and he condemned it at a local council in November of 448. He excommunicated Eutyches, and sent his decision to Pope Leo, who gave his approval in May 449.
Chrysaphius, who knew Eutyches personally, proceeded to use the monk as his instrument against the patriarch who had angered him. He convinced the emperor that a Church council should be convened to consider Eutyches' doctrine again. The resulting council, held in August 449 and led by Dioscorus of Alexandria, was completely illegitimate, and later formally condemned. But it pronounced against Flavian and declared him deposed from the patriarchate.