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Religious policy

Since Justinian was not the recognized head of any of the sects of the Christian church, his focus was on reducing or eliminating the friction between the various Christian sects and the Empire. As a Christian emperor, he believed he should be in harmony with the head(s) of the Church. Because Justinian was a Chalcedonian and Theodora was a Miaphysite (Non-Chalcedonian), Justinian worked to heal the divide between the Constantinople church and the Roman church. He wanted a united Church that would “partner” with one Emperor (himself); the Emperor would manage human affairs and the priesthood would manage the divine affairs of God. Since the Emperor was accountable to the law, Justinian ensured that the law recognized the Emperor as the law incarnate – with universal authority of divine origin. Consequently, he used the law to micromanage the implementation of religion through laws aimed at its very execution.

Theodora worked against her husband's support of Chalcedonian Christianity in the ongoing struggle for the dominance of each faction. As a result, she was accused of fostering heresy and undermining the unity of Christendom. However, Procopius and Evagrius Scholasticus suggested that Justinian and Theodora were merely pretending to oppose each other.

Theodora founded a Miaphysite monastery in Sykae and provided shelter in the palace for Miaphysite leaders who faced opposition from the majority of Chalcedonian Christians, like Severus and Anthimus. Anthimus had been appointed Patriarch of Constantinople under her influence and, after the ex-communication order, he was hidden in Theodora's quarters until her death in twelve years. When the Chalcedonian Patriarch Ephraim provoked a violent revolt in Antioch, eight Miaphysite bishops were invited to Constantinople; Theodora welcomed them and housed them in the Hormisdas Palace, Justinian and Theodora's dwelling before they became Emperor and Empress. Theodora persistently provided sanctuary for persecuted Miaphysites within the Palace, accommodating such a significant number of monks that, in one incident, several hundred gathered in a grand chamber, causing the floor to collapse. Furthermore, the Empress was instrumental in building the Church of Sergius and Bacchus, located next to Hormisdas palace. The dedicatory inscription, which remains visible to this day, proudly proclaims: ‘May he increase the power of the God-crowned Theodora whose mind is adorned with piety, whose constant toil lies in unsparing efforts to nourish the destitute.’

When Pope Timothy III of Alexandria died, Theodora enlisted the help of the Augustal Prefect and the Duke of Egypt to make Theodosius, a disciple of Severus, the new pope. Thus, she outmaneuvered her husband who wanted a Chalcedonian successor. However, Pope Theodosius I of Alexandria and the imperial troops could not hold Alexandria against Justinian's Chalcedonian followers; Justinian exiled the pope and 300 Miaphysites to the fortress of Delcus in Thrace.

When Pope Silverius refused Theodora's demand that he remove the anathema of Pope Agapetus I from Patriarch Anthimus, she sent Belisarius instructions to find a pretext to remove Silverius. When this was accomplished, Pope Vigilius was appointed in his stead.

In Nobatae, south of Egypt, the inhabitants were converted to Miaphysite Christianity about 540. Justinian was determined that they should be converted to the Chalcedonian faith, with Theodora equally determined that they should become Miaphysites. Justinian made arrangements for Chalcedonian missionaries from Thebaid to go with presents to Silko, the King of the Nobatae. in response, Theodora prepared her missionaries and wrote to the Duke of Thebaid, asking that he should delay her husband's embassy so that the Miaphysite missionaries would arrive first. The duke was canny enough to thwart the easygoing Justinian instead of the unforgiving Theodora. He made sure that the Chalcedonian missionaries were delayed; when they eventually reached Silko, they were sent away. The Nobatae had already adopted the Miaphysite creed of Theodosius.