It is clear that the demoralised and tired Greeks were no match for the Persians, and were completely routed in the battle which ensued at Ephesus. Many were killed, including the Eretrian general, Eualcides. The Ionians who escaped the battle made for their own cities, while the remaining Athenians and Eretrians managed to return to their ships and sailed back to Greece.

The Athenians now ended their alliance with the Ionians, since the Persians had proved to be anything but the easy prey that Aristagoras had described. However, the Ionians remained committed to their rebellion and the Persians did not seem to follow up their victory at Ephesus. Presumably these ad hoc forces were not equipped to lay siege to any of the cities. Despite the defeat at Ephesus, the revolt actually spread further. The Ionians sent men to the Hellespont and Propontis and captured Byzantium and the other nearby cities. They also persuaded the Carians to join the rebellion. Furthermore, seeing the spread of the rebellion, the kingdoms of Cyprus also revolted against Persian rule without any outside persuasion. Thus the Battle of Ephesus did not have a major effect on the revolt.