At the time of Justinian (who ruled between 527 and 565), the Christian world was divided by the Christological issue of how Christs nature should be understood. Either Christ had two separate (divine and human) natures (as the Pope and the West believed) or he had one single nature which combined these two elements.
In 451, the emperor Marcian had called the ecumenical Council of Chalcedon, in association with Pope Leo, to discuss this issue. 600 bishops, 3 papal legates and 2 delegates from Africa came to attend this gathering. The bishops decided that Christ was indeed of two natures. Some groups in the East, however, believed that this conclusion echoed the theology of Nestorius, whose ideas had been rejected at the earlier Council of Nicaea.
Justinian offered support for the Council of Chalcedon, and heavily restricted the freedoms of the anti-Chalcedonian opponents who sprung up in response to the meetings decisions. This persecution and limitation of expressive freedom solidified the anti-Chalcedonian cause, and disrupted any chance of unity across the Christian world, perhaps even more than the original Christological debate before the Councils attempted solution.
The Catholic Church
When the Goths, whose kings were not very interested in religious affairs, had taken Italy in the late 5th century, there developed a kind of cushioned independence for the Catholic Church. It could react autonomously, surrounded by Gothic kingdoms which were not really interested in its affairs.
Diplomatic efforts to break down these barriers were made by the emperor Justin I and his successor Justinian. Typified by the shared acceptance of Chalcedon, the Church thought the empire respected its authority. On the contrary, the Byzantines thought the Church was trying to reintegrate itself into the imperial world.
Authority of the Church vs Authority of the State
Justinian, however, sought to make theological pronouncements on his own authority, and this displeased the Catholic Church. Recorded in the Novels, part of a collection of law codes known as the Corpus Iuris Civilis, Justinian had rejected Pope Gelasius principle that the Church and State ought to have been mutually informing but ultimately separate parts of government. Gelasius believed that only Christ could compound the positions of priest and king, and the State should be “subordinate rather than superior to the religious order” (Letter from Gelasius I to Emperor Anastasius I). Justinian did not conform to this.
Furthermore, in order to appease aforementioned anti-Chalcedonians, Justinian condemned the “Three Chapters” of Theodore of Mopsuestia, Theodoret and Ibas – but served only to annoy the papacy, who believed the authority of Chalcedon was being questioned.
Regarding the older polytheistic religions, Justinian strongly persecuted any non-Christians: pagans and Jews were forbidden from holding office, and anybody who converted to a pagan cult was punishable with execution. Nonetheless, certain facets of paganism continued to exist during his reign.