Soon after the Conquest a determined resistance was made by many of the nobility against what they considered the tyranny of William. Led by such leaders as Edwin, Earl of Chester, Egelwyn, Bishop of Durham, and headed by Hereward, an English nobleman, they contrived to do considerable damage in the surrounding country. They built a castle of wood in the Fens, and made a vigorous stand against the Normans, who besieged the island, constructed roads through the marshes, threw bridges across the streams, and erected, as usual, a strong castle at Wiseberum. With the exception of Hereward, the rebellious subjects were reduced to submission. According to one authority, it is supposed that William's camp was simply an old Roman camp repaired for the occasion. We learn that the field, which contained the ancient site, was known as Belasis in some records of the reign of Henry III. It appears that one of William's generals was called Belasis, and that he was quartered on the monastery, which he had taken possession of after the conquest of the isle. He treated the monks with every mark of courtesy, allowing them to remain under an abbot of his own choosing. At first he laid them under certain restrictions, but subsequently restored the privileges they had previously been accustomed to.

In 1107 the eleventh and last abbot, Richard, employed all his interest with Henry I. and gained the royal sanction to the establishment of an episcopal see at Ely. To this the monarch granted, for a diocese, the county of Cambridge, which had till then been under the jurisdiction of the Bishop of Lincoln. The isle was also invested with sovereign powers. Richard, however, did not live to become the first bishop, an honour which was conferred in 1109 on his successor, Hervey.

By this arrangement the Abbot was superseded by the Bishop, and an entire distribution of the property belonging to the abbey was effected between them. As the abbey became the church of the See, the Abbot was obliged to alter his dignity to that of a prior. A fair, to continue for seven days, commencing from June 20, to commemorate the anniversary of the death of Ethelreda, was instituted by the Bishop. The prelate Nigel, in the reign of Stephen, built a castle here, of which no remains exist, and whose site is now conjectural. The year 1216 witnessed dreadful scenes of spoliation of churches and large sums of money exacted from the inhabitants under the guise of ransom.

The cause of all this devastation being visited upon Ely was John's idea of revenging himself upon the barons. At their hands he had, the year previously, been compelled to undergo the mortification of signing the Magna Charta at Runnymede, a field between Windsor and Staines. Ever since that time the irresolute and mean king had been devising schemes of vengeance against his opponents. Three months spent in the Isle of Wight had enabled him, through agents and the promise of the estates of the barons as plunder, to raise a considerable army of the Brabanters. At their head he suddenly emerged from concealment, and surprised the barons by appearing before Rochester Castle and defeating them.

In the meantime John was well supported at Ely by his general, William Bunk, or rather an unexpected incident hurried on its doom. The elements unkindly betrayed the city into the hands of the Brabanters. At a critical time, the treacherous swamps—the isle's hitherto great natural fortifications—became the city's undoing; for a sharp frost set in and rendered a ready glacial access to the city. The enemy lost no time in reducing the barons to submission and the wretched inhabitants to great misery. The barons, thus reduced to dire extremities, invited Louis, the eldest son of the King of France, to aid them, promising him through his wife the crown of England.