At the death of Bishop Keeton in 1316 the bishopric was conferred upon John Hotham (1316-1337), Chancellor of the Exchequer. Bentham calls him Prebendary of York and Rector of Collingham; Browne Willis calls him Provost of Queen's College, Oxford, and Chancellor of the University, and S.T.P., being the first bishop in his list who is credited with any university degree. He was a man of great eminence both as a bishop and as a statesman. In his political capacity he was Lord Chancellor. He was employed more than once on foreign embassies. He was one of the commissioners to arrange a truce between England and Scotland after the Battle of Myton in 1319, at which he had been present. He was made special commissioner to settle the troubles in Gascony. In his ecclesiastical capacity he added much landed property both to the see and the monastery. He erected the choir, providing for the building of the western bays after the fall of the tower. He obtained confirmatory charters from the king, and also a grant giving to the prior and convent the custody of the temporalities of the see during a vacancy, upon paying to the king, as long as their custody lasted, at the rate of £2000 a year. He died, "vir prudens, Justus, et munificus," in 1337.

The monks desired that their prior, John Crauden, should become bishop; but the king translated hither Simon Montacute (1337-1345), Bishop of Worcester. In a letter to the pope about him, in 1318, King Edward II. calls him his cousin (consanguineus). He materially assisted the buildings at the church, particularly the lady-chapel. He died in 1345.

Again the nomination of the monks, in favour of their prior, Alan de Walsingham, was set aside, and Thomas De Lisle (1345-1361) became bishop. He was prior of the Dominican Friars at Winchester. For nearly the whole of his episcopate he was engaged in a prolonged controversy with Lady Blanche Wake, a daughter of the Earl of Lancaster—the same lady who afterwards married John of Gaunt and became mother of King Henry IV. Her estates were contiguous to the bishop's manors in Huntingdonshire, and frequent disputes arose about their boundaries. The tenants took violent measures to assert the claims of their respective landlords, and much litigation ensued. The bishop, by his haughty behaviour, offended both the courts and the king, to whom he appealed; and at last he was constrained to escape to Avignon, then the seat of the pope. Here he had been consecrated; and here, while negotiations were proceeding for settling the dispute, in 1361 he died; and here he was buried.

This time the monks elected, not one of their own body, but the Dean of Lichfield. But once again their nomination was disregarded, and #Simon Langham# (1362-1366) was appointed bishop. He was Abbot of Westminster and Treasurer of England. He had lately declined the See of London. He was afterwards Lord Chancellor, and in 1366 he was translated to Canterbury; but he only remained archbishop till he was created a cardinal in 1368. In 1374 he was appointed Bishop of Præneste. Like his predecessor, he died and was buried at Avignon. This was in 1376. After three years his body was removed to Westminster Abbey, where his handsome monument is well known. The inscription implies that all the world sorrowed at his death: "Orbe dolente Pater ... ruit."

On his removal to Canterbury, the Bishop of Bath and Wells, John Barnet (1366-1373), was translated to Ely. He had been previously Bishop of Worcester, and for a time Treasurer of England. He "beautified" five of the windows in the presbytery. He died at Hatfield in 1373, but was buried at Ely.

His successor was Thomas Fitz-Alan (1374-1388), son of the Earl of Arundel, Archdeacon of Taunton. He is said at the time not to have been in holy orders and under twenty-three years of age. The convent had in vain elected the Archdeacon of Northampton. Bishop Arundel (so he is generally called) was Chancellor of England in 1386, but resigned that office in 1389, the year after he was made Archbishop of York. He ultimately became Archbishop of Canterbury, and died in 1414. He almost rebuilt the Bishop of Ely's palace in London. He fell into disfavour with King Richard II., and was banished; but he returned to England on the accession of King Henry IV. He was buried at Canterbury.

John Fordham (1388-1425), who succeeded Bishop Arundel at Ely, was Bishop of Durham. He had been Keeper of the Privy Seal. He died at Downham in 1425, and was followed by Philip Morgan (1426-1435), Bishop of Worcester. The king had given licence to the monks to elect, and had recommended his confessor. They elected instead their prior; but neither obtained the see. In Bishop Morgan's time the University of Cambridge secured entire freedom from the ecclesiastical jurisdiction of the Bishops of Ely: in the time of the previous bishop the University had got rid of the necessity of presenting their chancellor to the Bishop of Ely for confirmation. Bishop Morgan died at Hatfield in 1435, and was buried at the Charterhouse in London.

There was much dispute about the next bishop. The monks chose Fitz-Hugh, Bishop of London; but he died. The king then recommended the Bishop of S. David's; but the monks preferred Thomas Bouchier, Bishop of Worcester, whom the king refused. Bouchier appealed to the pope, who at first confirmed his election; but the bishop-elect was afraid to present the papal bull. This was an opportunity for the king (Henry VI.) "to gratify one of his numerous adherents of the French nation, who had lost their all in that kingdom, and followed his fortunes in this." He accordingly obtained the pope's consent to appoint #Lewis De Luxemburg# (1438-1443), Archbishop of Rouen, to be administrator of the Diocese of Ely, at the same time assigning him the £2000 a year due from the prior and convent to the king during a vacancy. The bulls for Bishop Bouchier's translation from Worcester were revoked. This was in 1438, which is held to be the beginning of Bishop Luxemburg's tenure of the see; but the spiritualities were not legally surrendered to him till the next year, and even then it seems to have been only under the title of "Perpetual Administrator of the See of Ely"; and in formal documents some time later he still has the same title, and even in the pope's bull appointing a new Bishop of Ely after his death. He had been Bishop of Terouanne, Chancellor of Normandy, and Governor of Paris, and was a great upholder in France of the cause of the King of England. He was afterwards cardinal. He was hardly ever in his diocese of Ely. He died at Hatfield in 1443, and was buried at Ely, his heart being taken to Normandy to be interred at Rouen.

There was now no opposition to the appointment of Thomas Bouchier (1444-1454), Bishop of Worcester. He was of the blood royal, being grandson of Thomas of Woodstock, Duke of Gloucester, son of King Edward III. He was not liked at Ely, where, after his installation, he would never take part in any solemn service. He became Archbishop of Canterbury in 1454, Lord Chancellor in 1455, and cardinal in 1464. He crowned three kings. He died in 1486 at his palace at Knole, and was buried at Canterbury.

He was succeeded by William Gray (1454-1478), Archdeacon of Northampton. He was for a time Treasurer of England and employed as Commissioner and Ambassador. He gave material assistance to the cost of the works at the west tower of the cathedral, and in various ways improved the presbytery. He was a great benefactor to Balliol College, Oxford. He died at Downham in 1478.