With the failure of the fifth crusade, people were looking for someone to blame. Emperor Frederick II of Germany was a popular target. He had taken the crusading vow during his coronation ceremonies in 1215, but with there being no active crusade at that time, he had no immediate obligation to fulfill. When the fifth crusade began, the emperor promised to take an active hand, but was unfortunately detained putting down a revolt in Italy. Though he did send his army to support the crusade, many feel that the effort would have succeeded had he gone in person.

Soon after the fifth crusade failed, Hermann von Salza, Grand Master of the Teutonic Knights, suggested that Frederick might regain his reputation by marrying Yolanda, the Queen of Jerusalem. It was an unhappy marriage that ending with Yolanda dying of childbirth complications six days after giving birth to Conrad, Frederick's son and heir. But politically, the marriage was quite successful, making Frederick King of Jerusalem and providing him with an heir.

Reaffirming his Crusader vow in the presence of the pope during 1223, Frederick set a date: June 24, 1225. Quickly realizing that he could not meet that deadline, Frederick once again reaffirmed his vow on June 25. This time he specified that he would provide one thousand knights, one hundred troop ship, and fifty fighting galleys. His entourage was to depart on August 15, 1227, and would fight for a minimum of two years.

Frederick was now on shaky ground, as Pope Gregory did not like him and believed him to be delaying out of cowardice. But the Emperor finally appeared to be serious, massing his army in the summer of 1227. Unfortunately, malaria broke out, but several thousand soldiers still departed in late July under the Duke of Limburg. Frederick was stationed at Brindisi, where the disease was rampant, but nevertheless managed to depart by September 8.

Frederick was hardly out of the harbor before he and several others aboard the ship fell ill with malaria. His advisors wanted him to dock and rest, but Frederick resisted for three days before relenting. When Pope Gregory heard of this, he immediately excommunicated Frederick for having yet again reneged on his vows.

Deciding not to let something like excommunication deter him, Frederick quickly amassed a second army, and once again set sail for the Holy Land in the spring of 1228. Pope Gregory was furious that the emperor had continued the Crusade without first being absolved of the excommunication, and promptly excommunicated Frederick again. This second excommunication bothered Frederick no more than the first.

Unfortunately, his excommunications took their toll. Many of his soldiers, troubled about following an excommunicated leader, found excuses to leave. The Hospitallers and Knights Templar flatly refused to help him. In fact, the only knightly order that would even consider aiding the emperor was the Teutonic Knights. By the time he reached Cyprus, Frederick was realizing that there would be no epic battles or legendary conquests on this crusade.

The prospect of a diplomatic conquest did not bother Frederick in the least, and so he tried to engage in parley with Al-Kamil, the Sultan of Egypt. The Sultan was somewhat ill disposed when the crusaders arrived, being in the middle of laying siege to Damascus. After having his underlings string out negotiations with the emperor for a few months, the Sultan decided to meet with Frederick.

They quickly came to an agreement, with Jerusalem being granted to the Christians, and both parties agreeing to a ten-year truce. Al-Kamil was criticized by his people for making this agreement, but he knew that he could retake the Holy Land whenever he wanted. Frederick was similarly criticized by the Christians, who protested that he was sent to kill the heathen, not dine with him and sign treaties. Additionally, they were now noticing the defensive vulnerabilities of Jerusalem that the Sultan had counted on when he made the deal.

The Emperor entered Jerusalem on March 17, 1229. On the next morning, Sunday, Frederick went to the Church of the Holy Sepulchre to celebrate mass, only to find that no priest was there. Undaunted, he proceeded to crown himself King of Jerusalem. This act, combined with the conquest that he represented, earned Frederick the hatred of most Palestinian barons. He had liberated Jerusalem and become its King, but it was immediately evident that his grasp on the Holy Land was tenuous at best.