In 1227 Frederick II sailed for the Latin East as had been agreed in 1225, but shortly afterwards he became ill and returned to Italy. Having recovered, he re-embarked, yet the delay created by his convalescence caused him to miss the deadline for departure which he had accepted in 1225. The new pope, Gregory IX, was not inclined to overlook this fact and in September 1227 he excommunicated the emperor. Shortly afterwards, Gregory began to prepare an invasion against Fredrick's kingdom of Sicily. Consequently, Frederick departed for the Levant in the full knowledge that war was brewing against him in the West. This fact overshadowed much of his subsequent expedition. Frederick landed at Limassol (northern Cyprus) on 21 July 1228. He was not the first excommunicate to travel on crusade; during the Fourth Crusade Conrad, bishop of Halberstadt, set off for the East in a similar predicament, seemingly in an attempt to gain absolution. Perhaps Frederick hoped that his departure would similarly cause Gregory to relent; if so, he was to be disappointed. Ironically, as Brundage has demonstrated, it was during the pontificate of Gregory IX that release from excommunication became ‘part of the bundle of privileges which crusaders regularly received’.

After his arrival in Cyprus, the emperor proceeded to impose his will upon the local nobility and arbitrarily demanded both the bailliage of Cyprus and possession of the city of Beirut from the influential baron John of Ibelin. These demands caused outrage and provoked the hostility of many of the local magnates. The emperor then took ship for Acre where, on 7 September 1228, he joined the main crusading army. In November he marched south to Jaffa, which he began to refortify.