By the end of the day on June 3, the crusaders controlled most of the city, except for the citadel, which remained in hands of Yaghi-Siyan's son Shams ad-Daulah. John the Oxite was reinstated as patriarch by Adhemar of Le Puy, the papal legate, who wished to keep good relations with the Byzantines, especially as Bohemund was clearly planning to claim the city for himself. However, the city was now short on food, and Kerbogha's army was still on its way. Kerbogha arrived only two days later, on June 5. He tried, and failed, to storm the city on June 7, and by June 9 he had established his own siege around the city.
More crusaders had deserted before Kerbogha arrived, and they joined Stephen of Blois in Tarsus. Stephen had seen Kerbogha's army encamped near Antioch and assumed all hope was lost; the deserters confirmed his fears. On the way back to Constantinople, Stephen and the other deserters met Alexius, who was on his way to assist the crusaders, and did not know they had taken the city and were now under siege themselves. Stephen convinced him that the rest of the crusaders were as good as dead, and Alexius heard from his reconnaissance that there was another Seljuk army nearby in Anatolia. He therefore decided to return to Constantinople rather than risking battle.