At the end of the twelfth century the minster was utterly unlike the present building. Except in the crypt, and in certain parts of the nave and tower not visible to the casual observer, there are no vestiges of the work of the earlier builders. There is now no Norman work to be seen in the minster itself, and in 1200, nave, choir, transepts, and towers were all Norman. Of these the transepts appear to have been the poorest part. They were probably short, and had no aisles. The nave also was of rude Early Norman character. The Early English architects having determined, probably, to rebuild the nave and transepts, made a beginning with the transepts about 1230. Roger's choir, only finished about fifty years before, no doubt seemed to them grand enough. The transepts were built on a totally different scale to the rest of the church as it then stood. They were both longer and broader, and they had aisles on each side of them. No doubt the object of this was to get a standard for the ultimate rebuilding of the nave. The greater width of these transepts made it difficult to join their aisles with those of the nave and choir, and were the cause of a curious and daring expedient, which will be described in the architectural account of the building. The south transept was the first to be rebuilt. It is the work of Walter de Gray, archbishop from 1216 to 1265, who was buried under an arch of his own building, in a tomb which still remains the most beautiful, perhaps, in the minster. The north transept seems to have been begun as soon as the south was finished; it is said to have been the work of John Romeyn, or the Roman, an Italian, and the treasurer of York. Walter de Gray probably also had a large part in the building of them. These transepts are the earliest part of the existing minster. John Romeyn also built an Early English central tower in place of Thomas's Early Norman tower. It remained for John Romeyn the younger, son of the treasurer, and archbishop from 1286 to 1296, to begin the rebuilding of the nave. It was planned on a far larger scale than the old nave, and was wider even than the Early English transepts. The old nave had been 83 feet wide, the transepts were 95, and the new nave 103. The difference in width between the transepts and the new nave is in the aisles. The plan of the transepts had no influence on the plan of the nave. The large triforium, small clerestory, and moderate-sized main arches give way to a large clerestory, large main arches, and practically non-existent triforium. These are unusual proportions in English Churches of that period. At Ely, Westminster, Beverley, and many other places, the proportions of Norman or Early English work influenced those of the later Decorated and Perpendicular.
The records of the building of the nave are somewhat scanty. Stubbs tells us that the foundation stone was laid on April 6, 1291, and that it was begun on the south side towards the east. It has been supposed that the chief object of making the new nave so much wider and loftier than its predecessor, was that it might be built round the old work without interfering with its utility.
But a petition, dated 1298, states that the old nave had long since fallen (diu est corruita). If this were so there was no object in refraining from disturbing the old work. It is uncertain whether the nave had been purposely destroyed, or had fallen of its own weight. It may be, though we have no record of the fact, that Thomas's Norman tower fell down, as did so many Norman central towers, destroying with it some part of the nave, and so made the rebuilding of that part of the church necessary.
The nave is fully developed geometrical Decorated work. It is loftier than the transepts, and its roof is low pitched. The main part of the rebuilding seems to have been done between 1298 and 1320. The indenture for glazing the great west window is still extant, and is dated 1338. The nave must have been roofed before this.
The vault was probably intended to be stone, but the great width of the building seems to have made the builders afraid, and they erected a vault of wood, but shaped and ribbed to look like stone. The outer walls of the clerestory, and the pinnacles of the south side of the nave show vestiges of flying buttresses. It is uncertain whether these were merely intended when a stone vault was projected, or whether they were actually erected, and afterwards, being unnecessary for the support of a wooden vault, were allowed to fall into disrepair. There are no flying buttresses on the north side, and the pinnacles are much smaller.
The west front was undoubtedly the latest part of the work to be finished, except the vault. The lowest stages, though geometrical in style, are later in character than the nave itself. The great west window, and the upper stages are of florid curvilinear Gothic. The west front is said to have been finished, and the great west window glazed by Archbishop Melton, who gave 500 or 600 marks to the fabric in 1338. The church was vaulted in 1354; Archbishop Thoresby is said to have given the wood. Before the beginning of the nave, the relics of St. William had been carried into the choir, and installed there with great pomp. The offerings of the faithful at his shrine helped to defray the expense of the building. Further funds were gained by means of indulgences granted by successive archbishops. The houses of Vavasour and Percy gave wood and stone, and statues of their representatives were placed over the main porch of the west front.
The date of the chapter-house, and the passage connecting it with the north transept is disputed. Browne thinks it was begun about 1280, and finished about 1340. He partly bases his contention on the fact that the Acts of the Chapter from 1223 to 1300 are given in Capitulo Eborum. After 1300 in Capitulo Ecclesiae, or in loco Capitulari ipsius Ecclesiae. After 1342 in domo Capitulari. From this he argues that up to 1342 the chapter-house was not in existence, or unfinished, but that it was in use from that date. The geometrical character of the tracery, and the Purbeck marble shafts used in the chapter-house might seem to support that view. Professor Willis, however, considers there is little significance in the difference in the phrases used. In capitulo simply means "in chapter," and in loco capitulari and in domo capitulari are vague phrases which may either mean a chapter-house, or a place used for the sittings of the chapter. At any rate, he thinks the chapter-house was not begun until after 1320, and the passage leading to it is still later. If this is the case, however, there is no reason why the chapter-house should not have been finished in 1342, and that would account for the change of phrase in the Acts. Though, at first sight, the building appears to be Early Decorated in style, on a closer examination it will be seen that the slender mouldings, the character of the carvings, and the details, especially on the outside, all point to a later date. It is curious, however, that if the building was not begun until after 1320, the tracery was not curvilinear, as in the great west windows, and the middle windows of the towers built about the same time. Perhaps, however, the geometrical forms were found to give the greater support, necessary owing to the absence of a central pillar. On the whole, the evidence of details, particularly of the foliage in the beautiful arcading inside the chapter-house, seem to point to its not having been begun until 1320 or later.