With the defeat of the Ionian fleet at the Battle of Lade, the revolt was effectively over. Miletus was closely invested, the Persians "mining the walls and using every device against it, until they utterly captured it". According to Herodotus, most of the men were killed, and the women and children were enslaved. Archaeological evidence partially substantiates this, showing widespread signs of destruction, and abandonment of much of the city in the aftermath of Lade. However, some Milesians did remain in (or quickly returned to) Miletus, though the city would never recapture its former greatness.

Miletus was thus notionally "left empty of Milesians"; the Persians took the city and coastal land for themselves, and gave the rest of the Milesian territory to Carians from Pedasus. The captive Milesians were brought before Darius in Susa, who settled them at "Ampé" on the coast of the Persian Gulf, near the mouth of the Tigris.

Many Samians were appalled by the actions of their generals at Lade, and resolved to emigrate before their old tyrant, Aeaces of Samos, returned to rule them. They accepted an invitation from the people of Zancle to settle on the coast of Sicily, and took with them the Milesians who had managed to escape from the Persians. Samos itself was spared from destruction by the Persians because of the Samian defection at Lade. Most of Caria now surrendered to the Persians, although some strongholds had to be captured through force.