In 1392 the Court of the King's Bench again sat at York. Richard II. visited the city several times. The archbishops Neville and Arundel played a great part in politics at this period. After the deposition of Richard II. a prebendary, by name Mandelyn, who bore a great resemblance to the king, personated him and headed a revolt, but he was captured and put to death. The chapter in general were strongly in favour of Richard, and three other prebendaries were imprisoned.
In 1405 occurred the rebellion, headed by Scrope, the archbishop. After he had been trapped and captured, the king had great difficulty in bringing him to trial, as the Chief Justice, Gascoyne, refused to try him. He was finally condemned in his own palace, at Bishopthorpe, and executed near to the walls of the city. Henry IV. withdrew also the liberties and privileges of the city, and the citizens had to beg for pardon on their knees with ropes round their necks. The archbishop was buried in the minster, and his tomb was much frequented by pilgrims in the north.
In 1407 the rebellion broke out again, and the citizens of York were again severely punished. In the fifteenth century the importance of York began to decline, and from that time it owes the position it still holds chiefly to its ecclesiastical eminence. Richard III. visited York several times, and gave a great cross to the minster, standing on six steps, each of which was ornamented with the figure of an angel. The figures were all of silver, and the whole was decorated with precious stones. Richard also planned the establishment of a college of 100 chaplains, and in 1485 six altars were erected for their use. But the scheme came to an end on the death of the king. York had been greatly devoted to Richard, but it submitted to Henry VII. when he made a state entry into the city in 1486, and it remained loyal in the rebellion of Lambert Simnel, when the rebels besieged the city, but were repulsed.
In the reign of Henry VIII. the importance of York was steadily declining. He only visited the city once. The whole of Yorkshire, which was no doubt poorer and more ignorant than most other counties, was much disturbed by the abolition of the monasteries and the spoiling of the churches, especially by the seizing of the head of St. William, the chief treasure of the minster. In 1536 the insurrection known as the Pilgrimage of Grace broke out, and the city willingly received the rebels. Aske, their leader, made a proclamation that all the "religions" should be reinstated in their old places: and the friars sang matins the same night. In 1557 Aske was hanged on a gallows set upon one of the bars of York. Henry entered York, and the citizens sued for pardon, which was not granted to them until 1560. Henry ordered the removal of such shrines as had not already been destroyed, and fragments of these have been found buried near the minster. Henry determined to establish his authority firmly in the north, and established the famous council which appointed the Duke of Norfolk their president. The council was held in the house of the Abbot of St. Mary's. It took away most of the powers of the Mayor and Corporation, but gave renewed importance to the city.
The diocese was much neglected during the episcopacy of Wolsey and his successor Lee. Both were statesmen rather than ecclesiastics. Indeed, it is said that Wolsey never set foot in York itself, though he was arrested at Cawood, where was one of the bishop's palaces. Lee was employed continually on missions and embassies. He happened to be in York, however, at the time of the Pilgrimage of Grace, and was seized by the rebels, carried to Pontefract, and compelled to swear support to the rebellion. The see was much impoverished in the time of Holgate, Lee's successor (1545-1554), who supported Henry in his quarrel with the Pope.
Much of the property taken by Henry was restored by Mary to Heath, the next archbishop, who was the last appointed by a papal bull with the acknowledgment of the Government. Heath was deposed by Elizabeth in 1559.
In 1569 occurred another rising in the north in favour of the old religion and of Mary Queen of Scots, under the Earls of Northumberland and Westmoreland.
In Richmondshire and the Cleveland district the new prayer-books were destroyed, and the old service restored. York itself favoured the rebels, but before it could be entered a force arrived from the south and the rebellion sank to nothing. The queen's army exacted a loan of £500 from the citizens of York. Eleven persons also in the city were sentenced to death. The Earl of Northumberland also was afterwards executed and buried in York. After the rebellion the Roman Catholics in the diocese were much persecuted. They were forced to attend the reformed services and the Holy Communion, and their priests were hunted down. Attempts also were made to abolish the Christmas mummeries and the miracle plays. The archbishop of this period, Thomas Young, is accused of plundering the estates of the church in the interests of his own family.
Charles I. had a great affection for the city and minster of York, and enriched the latter with many gifts. For instance, he gave £1000 to the chapter for the building of a new organ, and out of the same the chapter also bought some Communion plate, and a Bible and prayer-book richly bound in purple velvet and ornamented with silver-gilt plates. These latter are still preserved. He further removed certain houses and offices which had been built close to the west and south doors. He also destroyed a building which had been erected inside one of the transepts, and ordered certain seats in the choir, which hid the stalls and woodwork, to be taken away.
Charles also wrote to the Corporation in 1639, ordering them not to bring the official sword and mace into the minster, and to receive the Holy Communion there on certain fixed occasions. The Mayor and Corporation evaded the order by entering the church with sword and mace "abased." They have never yet officially attended Holy Communion. They also had a quarrel with the dean and corporation owing to their practice of using the north aisle of the nave, known as the Lord Mayor's Walk, as a common promenade. The dean and chapter endeavoured to put a stop to this in 1632, but it continued until the end of the century.