Even though the Empire had gained smaller successes over the Slavs and Avars in pitched battles across the Danube, both enthusiasm for the army and faith in the government had lessened considerably. Unrest had reared its head in Byzantine cities as social and religious differences manifested themselves into Blue and Green factions that fought each other in the streets. The final blow to the government was a decision to cut the pay of its army in response to financial strains. The combined effect of an army revolt led by a junior officer named Phocas and major uprisings by the Greens and Blues forced Maurice to abdicate. The Senate approved Phocas as the new Emperor and Maurice, the last emperor of the Justinian Dynasty, was murdered along with his four sons.

The Persian King Khosrau II responded by launching an assault on the Empire, ostensibly to avenge Maurice, who had earlier helped him to regain his throne. Phocas was already alienating his supporters with his repressive rule (introducing torture on a large scale), and the Persians were able to capture Syria and Mesopotamia by 607. By 608, the Persians were camped outside Chalcedon, within sight of the imperial capital of Constantinople, while Anatolia was ravaged by Persian raids. Making matters worse was the advance of the Avars and Slavic tribes heading south across the Danube and into Imperial territory.

While the Persians were making headway in their conquest of the eastern provinces, Phocas chose to divide his subjects rather than unite them against the threat of the Persians. Perhaps seeing his defeats as divine retribution, Phocas initiated a savage and bloody campaign to forcibly convert the Jews to Christianity. Persecutions and alienation of the Jews, a frontline people in the war against the Persians helped drive them into aiding the Persian conquerors. As Jews and Christians began tearing each other apart, some fled the butchery into Persian territory. Meanwhile, it appears that the disasters befalling the Empire led the Emperor into a state of paranoia — although it must be said that there were numerous plots against his rule and execution followed execution.