The alterations and additions during the Perpendicular period can be detected at a glance. All the Norman windows which had remained unaltered were now filled with tracery, not of particularly good design; the great west window and the others in the west wall were similarly treated; the conical tops to the transeptal corner turrets were altered into battlements; the screens in the transepts were made, and, probably, the groined wooden ceiling in the choir. The most important addition was the New Building at the east end of the choir. This is often erroneously called the Lady Chapel; but when this edifice was erected the Lady Chapel to the east of the north transept, and for more than 150 years afterwards, was still standing. The new building was begun by Abbot Ashton (1438-1471), and finished by Abbot Kirton (1496-1528). The rebus of each of these abbots can be seen in its decorations: an ash growing out of a tun or barrel, and a church or kirk with a tun.
In 1540 the reign of the abbots came to an end, and in 1541 the church became a cathedral. For a hundred years the church itself, as well as all the buildings attached to it, appear to have remained in their full glory. There is no reason to discredit the account given of the preservation of this church, when so many others were dismantled or sold at the suppression of the monasteries. It was suggested to King Henry VIII, after the interment here of Queen Katharine of Aragon, that it would become his greatness to erect a suitable monument of her in the place where she was buried; and in reply the King said he would leave her one of the goodliest monuments in Christendom, meaning that he would spare the church for her sake. We conclude, however, from what we know of the state of the fabric in the reign of Charles I, that although no buildings may have been demolished, yet the church itself was falling into disrepair. No doubt the diminished resources of the establishment, as well as the numerous demands upon the stipends (never large) of the members of the chapter, most of whom had duties and claims elsewhere besides having families to support, materially reduced the amount that could be annually devoted to the sustentation of the fabric. In the time of the civil war much wanton destruction took place. Nearly everything in the nature of ornamentation or embellishment was destroyed. A full account of the mischief wrought has been preserved. Without particularly naming such things as books, documents, vestments, and the movable ornaments, we find the damage done to the fabric itself was terrible indeed. The organs, "of which there were two pair," were broken down. All the stalls of the choir, the altar rails, and the great brass chandelier, were knocked to pieces. The altar of course did not escape. Of the reredos, or altar-piece, and its destruction, Patrick writes as follows: "Now behind the Communion Table, there stood a curious piece of stone-work, admired much by strangers and travellers; a stately skreen it was, well wrought, painted and gilt, which rose up as high almost as the roof of the church in a row of three lofty spires, with other lesser spires, growing out of each of them, as it is represented in the annexed draught.[[15]] This had now no Imagery-work upon it, or anything else that might justly give offence, and yet because it bore the name of the High Altar, was pulled all down with ropes, lay'd low and level with the ground." All the tombs were mutilated or hacked down. The hearse over the tomb of Queen Katherine was demolished, as well as the arms and escutcheons which still remained above the spot where Mary Queen of Scots had been buried. All the other chief monuments were defaced in like manner. One in particular is worth mentioning. It was a monument in the new building erected to himself by Sir Humfrey Orme in his lifetime. Two words on the inscription, "Altar" and "Sacrifice," are said to have excited the fury of the rabble, and it was broken down with axes, pole-axes, and hammers. So this good old knight "outlived his own monument, and lived to see himself carried in effigie on a Souldiers back, to the publick market-place, there to be sported withall, a Crew of Souldiers going before in procession, some with surplices, some with organ pipes, to make up the solemnity." This monument, as it was left after this profanity, is still to be seen exactly as it remained when the soldiers had done their work. The brasses in the floor, the bells in the steeple, were regarded as lawful plunder. The same would not be said of the stained glass, of which there was a great quantity. This was especially the case with the windows in the cloisters, which were "most famed of all, for their great art and pleasing variety." All the glass was broken to pieces. Much that escaped the violence of these irresponsible zealots fell before the more regular proceedings of commissioners. By their orders many of the buildings belonging to the cathedral were pulled down and the materials sold. This was the case with the cloisters, the chapter-house, the Bishop's hall and chapel. The merchant that bought the lead from the palace roofs did not make a very prosperous bargain, for he lost it all (as Dean Patrick says, within his own knowledge) and the ship which carried it, on the voyage to Holland.
For some time nothing was done to repair the damage. At length the Chief Justice of the Common Pleas, Oliver St. John, obtained a grant of the ruined Minster, which he gave to the town for use as a parish church, their own parish church having also gone to decay. This gentleman was doubly allied to the Cromwell family, his first wife being great-grand-daughter of Sir Henry Cromwell, of Hinchinbrooke, and his second wife daughter of Henry Cromwell, of Upwood. He had been sent upon a distasteful embassy to Holland, where he experienced many indignities; and on his return, according to Mark Noble,[[16]] "he protested, that all the favour which he received in reward for this embassy, was, that he obtained the cathedral of Peterborough, which was propounded to be sold and demolished, to be granted to the citizens of that place." The interest that he took in Peterborough arose from the fact that he resided at Longthorpe Hall, about two miles off.
The burden of restoring the church to a decent condition being too great for the inhabitants, they agreed to pull down the Lady Chapel, and sell the materials. This was done, except that some portion of the woodwork was utilised in repairs. The painted boards from the roof were made into backs for the seats in the choir. An engraving of the choir as it appeared in the eighteenth century shews these boards. They are mostly adorned with the letter M surmounted by a crown, and the three lions of England, in alternate lozenges. Until the Restoration the church was served by a school-master of the Charterhouse, Samuel Wilson, appointed by the London Committee. When the cathedral body was restored, further repairs were gradually effected, and when Dean Patrick wrote, he says that the church was "recovering her ancient beauty and lustre again."