The period of peace was disrupted during the 7th and 8th centuries when raids began. In the 9th century Crete was attacked by the Arabs, who settled and established the new capital, Chandax (present day Heraklion), to the west of the harbour of Minoan Knossos, which, until then, had been a small insignificant port, clearly less important than Amnissos, which had operated as the port for Knossos during the peak years of the palace. So, suddenly, with the arrival of the Arabs, Chandax acquired an urban character and became the centre of Crete.

Thus began the Arab reign that lasted a century and a half, during which Crete became the base of the Saracen pirates in eastern Mediterranean. Local Christian populations were persecuted but continued to survive, especially in the mountains.