Soon after the Norman Conquest, the church of St. Olave, with four acres adjoining, was given by the Earl of Richmond to Stephen of Whitby to found a Benedictine monastery. The site, however, was church property, and the Archbishop only relinquished it when William II gave him an equivalent. King Rufus laid the foundation stone of the abbey church, which was dedicated to St. Mary. The foundations of the eastern part of this church have been laid bare and show the apsidal terminations.

The introduction into England of the Cistercian order, with their stricter rule of conduct, led some of the monks of St. Mary’s to attempt a raising of the standard of discipline in their own monastery. The other monks, however, resented their interference. The reformers, filled with admiration of the accounts they heard of the holy lives led by the inmates of the Cistercian house of Rievaulx, were now anxious to found a colony of that order and communicated their desire to the Abbot of St. Mary’s, who, however, refused to allow them to leave, as it would bring discredit on his abbey. The reformers included the prior, sub-prior, sacrist, almoner, and precentor. The prior consulted the Archbishop, who decided to hold a visitation at the abbey.

Archbishop Thurstan on the day appointed rode to the abbey gatehouse attended by the Archdeacon of York, the Minster Treasurer (afterwards St. William), the Prior of Guisborough, and the Master of St. Leonard’s Hospital. Leaving their horses at the gateway, they walked to the chapter house and were received by the abbot, who protested against anyone entering but the Archbishop and his clerks. The Archbishop remonstrated, but the monks who had filled the chapter house, considering it was a Cistercian attack on their own order, created an uproar by hooting and screaming and prevented the Archbishop being heard; he, however, in a lull shouted, “I place the Abbey under an interdict.” “Interdict it for a hundred years,” exclaimed one of the monks, and then arose the cry of “Catch them!” The Archbishop with his retinue and the thirteen reformers were alarmed and took refuge in the church, and after a time were permitted to leave the abbey.

The Archbishop befriended the outcasts and subsequently gave them a plot of ground, near his manor at Ripon, on which they founded the Cistercian Abbey of Fountains.

Simon of Warwick became Abbot of St. Mary’s in 1259, and placed it in greater security from the attacks by the citizens, between whom and the monks were often quarrels, owing to the privileges claimed by the abbey. The monastery, being just outside the city, was always in danger from raiding expeditions of the Scots, so in the year 1266 the abbot had licence from the king to wall in the abbey close.

Abbot Warwick in 1271 laid the foundation stone of a new church to St. Mary’s Abbey. He began by building at the rear of the Norman church a new aisled choir of nine bays. The Norman edifice was then taken down and replaced by a new aisled nave of eight bays, transepts of three bays with eastern aisles, and lofty tower with spire. The western front has a central doorway set between arcading; the doorway jambs are delicately sculptured with the ivy and its trailing stem. The aisle windows are alternately of two and three lights with geometrical tracery and placed above an arcade—the work is similar to that in the north aisle of the choir at Selby Abbey. One of the views depicts the eastern archway with clerestory of the nave north aisle. The remains of the church show it to have been a magnificent example of the art of the last quarter of the thirteenth century. Excavations have revealed the foundations of the choir and exhibit the full length of the church.

The ruins of the vestibule and entrance to the chapter house are beautiful examples of the richly ornamented late Norman work.

The walls of the abbey close remain. The principal, and for a long time the only entrance, was that of Mary Gate. There is a fine arch and on either side of the gateway is an arcade with stone seats. The vaulted roof and the courtroom above for the Liberty of St. Mary have disappeared. The gatehouse adjoins and is now a private dwelling. John Phillips, the eminent geologist, resided in it for some years. On the opposite side are the ruins of the Chapel of Our Lady at the Gate; the edifice was of two stories, with the chapel on the first floor which was reached by a stone stair.

The Bootham entrance was made in order to shorten the distance from the abbot’s house to the Minster, and in expectation of a visit of Henry VII, on his return from Scotland. The Princess Margaret, daughter of Henry VII, was the guest of the Lord Abbot of St. Mary’s for two days on her journey to the north to be the bride of James IV of Scotland. The Princess, accompanied by five hundred lords and ladies, was met at Tadcaster Bridge by the Sheriffs in crimson gowns, attended by one hundred persons on horseback, who conducted her royal highness towards the city. At Micklegate Bar, the Princess was received by the Lord Mayor and Corporation, who welcomed her to the city. On the following day the Lord Mayor and Corporation waited upon the Princess, and presented her with a silver gilt cup containing one hundred angels of gold for which she heartily thanked them. The next day the Lord Mayor, Sheriffs, and Aldermen escorted the Princess as far as Magdalene Hospital in Bootham. The Lord Mayor made a long oration in taking his leave, to which the Princess replied, “My Lord Mayor, your brethren, and all the whole city of York. I shall evermore endeavour to love you and this city all the days of my life.”

The Bootham entrance to St. Mary’s Abbey consists of an archway with porter’s lodge now used as a shop. From here the abbey walls continue behind the houses to the circular tower at the end of Marygate. The tower contained the records of many of the suppressed northern monasteries. During the siege of York in the time of the Great Civil War, one Sunday the Parliamentarians having laid a mine, blew up the tower and entered the grounds. The Royalists sent out a body of men by the Watergate and up Marygate to the ruined tower. Those inside were thus caught and were compelled to surrender. The tower was afterwards rebuilt, but on a smaller scale. From the tower the abbey walls stretch to the gatehouse and from there continue to the river, where they terminate in a circular tower, which is seen in the view taken across the river from near the railway bridge.