During the Civil War York suffered less than many cathedral cities. In 1644 it was besieged by the Parliamentary troops and the Scots under Fairfax and Leslie. During the siege the minster seems to have been spared as far as possible, mainly, perhaps, through the influence of Fairfax, but it did not escape entirely scatheless. Thomas Mace, the author of "Musick's Monument," was in the city during the siege, and he thus describes the way in which the minster suffered:—"The enemy was very near and fierce upon them, especially on that side the city where the church stood; and had planted their great guns mischievously against the church; with which constantly in prayer's time, they would not fail to make their hellish disturbance by shooting against and battering the church; insomuch that sometimes a cannon bullet has come in at the windows and bounced about from pillar to pillar (even like some furious fiend or evil spirit) backwards and forwards and all manner of sideways, as it has happened to meet with square or round opposition amongst the pillars."
During the siege the citizens suffered much from the presence of the soldiery who were billeted upon them. Each citizen, in addition to giving free quarters to as many soldiers as possible, had to pay £2 a month for their support. The siege lasted for six weeks, and in the course of it the Marygate Tower, which was used as a record office for the whole of the north, was attacked and spoiled, all the records in it, an irreparable loss, being destroyed. The city was captured soon after Marston Moor, and the defenders obtained very good terms, marching out with all the honours of war. The citizens also were well treated. They were to enjoy all their old privileges and were to be preserved from plundering. All churches and public buildings were to be treated with respect. A Presbyterian service was at once held in the minster by the conquerors. The Corporation presented to Fairfax a butt of sack and a tun of French wine in gratitude for the good offices he had rendered them. There can be little doubt that the great amount of stained glass still remaining in the minster is owing to the control he exercised over the Parliamentarians. On October the 24th of the same year the Corporation ordered that the Solemn League and Covenant should be tendered to the aldermen and citizens. Then all the Royalist members of the Corporation were removed, and both the bishop, Williams, and the dean, Scott, were deprived of their offices. They left the country, and the dean died in a debtor's prison in 1646. Fairfax, however, who remained as governor of the city, maintained the minster in scrupulous repair, and paid all the salaries of the necessary officials. A short time before the Restoration a large sum of money was spent on the bells. It has been said, indeed, that the Puritans wished to pull down the chapter-house, but there is no authority for the statement. But the control of the minster was taken out of the hands of the chapter and given to the Corporation, and this transference was only effected by the interference of the troops. The organ given by Charles was also taken down, and silver candlesticks and other ornaments, including the brass about the shrine, perhaps, of St. William, and also the lectern in the choir, were sold for the repair of the fabric and bells. In 1646 the organ loft, the canopies over the altar in the side choir, and the font were removed. In 1647 a cushion was made of the dossal. The library was left untouched and thrown open to the public, and the keys of the minster placed in charge of the Mayor and Corporation. In place of the dean and chapter, the precentor, and chancellor—all removed—four city preachers were chosen by the Assembly of Divines, and paid out of the revenues of the minster. Meanwhile the churches in the city suffered far more than the minster itself. In 1646 all "superstitious pictures in glass" and images were ordered to be broken, and the fonts were removed. In 1648 twenty-four churches in the city were without incumbents.
After the Restoration the Corporation did everything in their power to resist a return to the old order of things, and in 1663 there was a small rebellion, as a result of which twenty-one persons were executed at York. Discontent, however, continued, and in 1682 it became necessary to appoint Sir John Reresby governor of York, with a garrison of 500 men. The governor said that York was one of the most factious towns in the kingdom. About this time, also, the dean and chapter caused a riot by issuing a proclamation forbidding the nave to be used as a promenade. They succeeded, however, in finally putting an end to the practice.
In 1686 Lady Strafford, daughter-in-law of the great Strafford, was buried in the minster. Party spirit still ran very high, and the mob rushed at the hearse and endeavoured to tear the coats of arms from it. The military was called out, and there was a sharp struggle in the minster itself.
The Catholic designs of James II. were ill received in York. His proclamation for liberty of conscience was read in hardly any of the York churches, and an attempt to stock the Corporation with Roman Catholics was resisted. At last there came a crisis. The king appointed James Smith, the Roman Catholic Bishop of Callipolis, one of his four vicars-apostolic, and in August 1688 he appeared at York. The archbishopric had been vacant for two years, and it was rumoured that the king intended to appoint Smith to the see.
York, therefore, was ripe for the revolution, and it broke out there on November 22. Lamplough of Exeter, a discreet and timely supporter of both James and William, was appointed archbishop, and Smith was attacked by the mob as he was passing through the streets in procession. His silver-gilt crozier, which had been given to him by Catharine of Braganza, was torn from him and sent to the vestry of the minster, where it still remains. It is seven feet in length. Smith fled to Wycliffe-on-Tees, where he spent the rest of his life.