Abstract This paper offers an analysis of the dynamics at play in an under-studied episode of religious violence in Late Antiquity, the so-called ‘pagan affair’ which took place in 580 during the reign of Tiberios. It provides a novel explanation for why the Chalcedonian patriarchs Gregory of Antioch and Eutychios of Constantinople were targeted as pagans or sympathisers of pagans during the riots which erupted after the discovery of pagan circles among the Roman elite. The position of both of them was challenged: Eutychios held controversial theological views; moreover, he had previously been deposed and replaced by John Scholastikos, and many clerics considered his return to the episcopal throne uncanonical. Gregory was confronted with a similar difficulty, since his predecessor Anastasios had been sent into exile, but still had many supporters. In addition, both patriarchs were persecutors of the anti-Chalcedonians, who were therefore interested in slandering their persecutors in order to avenge themselves. The paper argues that charges in the form of anti-pagan polemic, such as those brought forth against the two patriarchs, were a useful weapon to deploy against political or religious opponents. It also sets the pagan affair in the context of Tiberios’ religious policy and analyses the strategies the emperor used to end the riots. Finally, it establishes a connection between the affair and an instance of pagan persecution which was triggered some years later, at the beginning of the reign of Maurice, by the successor of Eutychios, patriarch John the Faster.