The emperor Justinian I faced a major Samaritan revolt in 556. On this occasion the Jews and the Samaritans seem to have made common cause, beginning their rebellion in Caesarea early in July. They fell upon the Christians in the city, killing many of them, after which they attacked and plundered the churches. The governor, Stephanus, and his military escort were pressed hard, and eventually the governor was killed, while taking refuge in his own house. Amantius, the governor of the East was ordered to quell the revolt, after the widow of Stephanus reached Constantinople.

Despite the Jewish participation, the rebellion seems to have gathered less support than the revolt of Ben Sabar. The Church of the Nativity was burned down, suggesting that the rebellion had spread south to Bethlehem. Either 100,000 or 120,000 are said to have been butchered following the revolt. Others were tortured or driven into exile. However, this is probably an exaggeration as punishment seems to have been limited to the district of Caesarea.