He was succeeded by Eustace (1198-1215), Archdeacon of Richmond, Treasurer of York, Dean of Salisbury, and Keeper of the Great Seal. He was one of the bishops to whom was entrusted the invidious employment of publishing the excommunication of King John and putting the kingdom under an interdict. For this, in 1209, he was outlawed, and had to leave the country. Upon the king's submission in 1213, he (with Archbishop Stephen Langton and three other bishops) returned to England. He built the galilee at the west end of the church. He died in 1215 at Reading.

Robert of York was chosen by the monks to succeed him. They had at first selected Geoffrey de Burgh, but for some reason that does not appear they altered their minds before making their selection known. Robert got possession of the temporalities, and even gave away preferments that were in the bishop's gift, for five years; but the king never consented to his appointment, nor was he ever consecrated. He took the part of the French against the king, who at last applied to the pope to nominate some one else to the See of Ely. Accordingly, upon the recommendation of the Archbishop of Canterbury, the Legate Pandulph, and the Bishop of Salisbury, who had been authorised by the pope to make the selection, John Pherd (1220-1225), Abbot of Fountains, hence called De Fontibus, was made bishop. He was also Treasurer of England. He died at Downham in 1225, and was succeeded by the same Geoffrey De Burgh (1225-1228) who had at first been elected by the convent upon the death of Eustace. He was Archdeacon of Norwich, and brother to Hubert de Burgh, Earl of Kent. He gave much costly plate to the monastery, as well as three hundred acres of land.

Upon his death, Hugh Norwold or Northwold (1229-1254), Abbot of Bury S. Edmunds, became bishop. He had been a justice itinerant. He was one of the embassy sent to conduct to England the king's bride, Eleanor of Provençe. "He was one of the most eminent examples of piety and virtue in his time." He is especially commended for his hospitality and liberality to the poor; and he was a great benefactor to the monastery. He spent more than £5000 on the fabric of the church, and built the palace. The six eastern bays of the presbytery are his work. After removing to this new part of the church the remains of the three sainted abbesses and S. Withburga and also the so-called relics of S. Alban, he dedicated the whole church on September 17th, 1252, in the presence of King Henry III. and his son, Prince Edward. Bishop Norwold died at Downham in 1254, and was buried at the feet of S. Etheldreda, where a splendid monument was erected over his body, now removed to the north side of the presbytery, beneath the third arch from the east.

The next bishop was William De Kilkenny (1255-1256), Archdeacon of Coventry and chancellor of the king. After his consecration, which took place ten months after his election, he only lived thirteen months. He was consecrated by Archbishop Boniface at Belley, in Savoy, a place near the Rhone, about forty miles east of Lyons. He died in Spain while negotiating a treaty, and was there buried, at Sugho. His heart was brought to Ely.

Hugh Belsham (1257-1286) the sub-prior, came next. He founded Peterhouse (now S. Peter's College) at Cambridge. He had been elected in defiance of the king's recommendation, and the king tried to annul his election; but he proceeded to Rome, and was actually consecrated there by the pope. It is in connection with his election that we learn that the custom of the monks was to depute the election of a bishop to a committee of seven chosen from among themselves. Bishop Hugh died at Doddington in 1286.

The next bishop, John Kirkby (1286-1290), although at the time of his appointment Dean of Wimborne, Archdeacon of York, and Canon both of Wells and York, was only in deacon's orders. He was accordingly ordained priest one day and consecrated bishop the next. Three years previously he had been elected to the See of Rochester, but had declined it. He had also been Chancellor and Treasurer of England. He gave to his successors a house in Holborn, which formed the nucleus of the grand palace afterwards erected, adjacent property being subsequently acquired. He died in 1290.

His successor, William De Louth (1290-1298) was not even in holy orders at all when elected; yet he held prebends at S. Paul's, York, and Lincoln, the Archdeaconry of Durham, and the Deanery of S. Martin's-le-Grand. He is the only Bishop of Ely who was consecrated at Ely (it was in S. Mary's Church, not the cathedral), a provincial council of bishops happening to meet there at the time.

Ralph Walpole (1299-1302), Bishop of Norwich, was, on the death of Bishop Louth in 1298, translated to Ely; the prior, John Salmon, who had been elected by the monks, being made instead Bishop of Norwich. Walpole had been formerly Archdeacon of Ely. He revised the statutes of the monastery during the short time that he held the see, which was less than three years.

The next bishop, Robert Orford (1302-1310), like his predecessor, Hugh Belsham, was consecrated at Rome, though not, as he had been, by the pope himself. The Archbishop of Canterbury had refused his consent to the appointment on the ground that the elect was illiterate, but the pope overruled the objection. He died at Downham in 1310.

A monk of the house, John Keeton (1310-1316), succeeded. King Edward II. visited Ely in his time, and while there settled the controversy between Ely and S. Albans as to the true place where the body of the proto-martyr of England was deposited. The remains of S. Alban had been carried off to Denmark by the Danes, after plundering the abbey raised to his honour, and recovered by a trick. At a later time, fearing again an attack from the Danes, the Abbot of S. Albans sent to Ely a chest containing (so he said) the relics of the martyr for safe custody. When the troubles were over, the monks of Ely sent back the chest, but with other bones in it, supposing that they had thereby secured the true relics for their own church. So the Abbot of S. Albans declared that they were not the true relics that he had sent to Ely, but that he had buried them in a fresh place in his own church. The king, in 1314, decided the matter in favour of S. Albans.