Robert of Ramsey (1353-1361) ruled for eight years, and nothing else is known about him.

Henry of Overton (1361-1391) was abbot during the commotions in King Richard II.'s reign. The tenants with others rose up against the abbey, intending to destroy it. The Bishop of Norwich "coming to the assistance of the monastery with a strong power, forced the villains to desist from their enterprise: nay, dispersed them, and took some of them, and killed others; the rest, taking the church for sanctuary, which they intended to have destroyed, were there run through with lances and swords; some of them hard by the altar, others by the walls of the church, both within and without."

Nicholas (1391-1396), William Genge (1396-1408) the first mitred abbot, John Deeping (1408-1438) in turn succeeded. Nothing remarkable is told of them. The name of the last and the names of the next two are really the names of places; but the prefix "de" seems now to have been discontinued, and the place-name to have become a surname. Abbot John resigned his office the year before he died.

Richard Ashton (1438-1471) took great pains about the regulation of the services in the church, and drew up a customary out of the ancient usages of the place.

William Ramsey (1471-1496) appears to have devoted his time to the management of the estates and to upholding the territorial privileges of the house. If the epitaph formerly to be seen on a brass on his tomb is to be believed, he was a man prudent, just, pious, esteemed by all, chaste, kind, and adorned with every virtue.

Robert Kirton (1496-1528) has left several proofs of his energy in building, signing, as it were, the stones with his autograph. His rebus, a kirk on a ton, sometimes accompanied by the initial of his Christian name, is to be seen in the New Building, which he completed, on the Deanery gateway, and on the graceful oriel window in the Bishop's Palace. The chamber to which this window gives light still retains the name originally given of "Heaven's Gate Chamber." Much other work done by him towards the beautifying of the church and buildings has perished.

The last abbot was John Chambers (1528-1540). One incident of considerable interest is related as having taken place in his first year. "Cardinal Wolsey came to Peterburgh, where he kept his Easter. Upon Palm Sunday he carried his palm, going with the monks in procession, and the Thursday following he kept his Maundy, washing and kissing the feet of fifty-nine poor people, and having dried them, he gave to every one of them 12d. and three ells of canvas for a shirt; he gave also to each of them a pair of shoes and a portion of red herrings. On Easter day he went in procession in his cardinal's vestments, and sang the High-Mass himself after a solemn manner, which he concluded with his benediction and remission upon all the hearers." This abbot was a native of Peterborough, and was sometimes known as John Burgh; and on the brass placed on his tomb he was called "Johannes Burgh, Burgo natus." A monumental effigy was also erected to him, "made of white chalkstone"; and this is almost certainly the figure now placed (temporarily) at the back of the apse. This abbot was B.D. of Cambridge and one of the king's chaplains. It was during his time that Queen Katherine of Arragon was interred in the minster. The well-known story that the building was spared by the king out of regard to the memory of his first wife is told by Dean Patrick in these words:—[[34]]"There is this traditional story goes concerning the preservation of this church at the dissolution of abbeys: that a little after Queen Katherine's interment here (which Mr G. mentions), some courtiers suggesting to the king how well it would become his greatness to erect a fair monument for her, he answered, 'Yes, he would leave her one of the goodliest monuments in Christendom,' meaning this church, for he had then in his thoughts the demolishing of abbeys, which shortly after followed." Abbot Chambers surrendered the monastery to the king in 1540, and was appointed guardian of the temporalities, with a pension of £266, 13s. 4d. and 100 loads of wood. The king divided the whole property of the abbey into three parts, retaining one-third for himself, and assigning the other parts upon the foundation of the see to the Bishop and Chapter respectively. If the annual value of the portion he reserved for his own use may be taken to be exactly one-third of the possessions of the abbey, the entire property must have been worth as nearly as possible £2200 per annum. The last abbot became the first bishop.

It is remarkable that of the two queens buried at Peterborough, the body of one has been removed to Westminster by the orders of her son, and that a similar removal had been previously designed for the body of the other. Queen Katherine's daughter, Queen Mary, left directions in her will that "the body of the virtuous Lady and my most dere and well-beloved mother of happy memory, Queen Kateryn, which lyeth now buried at Peterborowh," should be removed and laid near the place of her own sepulture, and that honourable monuments should be made for both. It would have been a singular coincidence if this intention had been carried out.