After the Norman Conquest the church came into the possession of the Anglo-Breton magnate Alan Rufus who granted the lands to Abbot Stephen and a group of monks from Whitby.

The abbey church was refounded in 1088[3][4] when the King, William Rufus, visited York in January or February of that year[5] and gave the monks additional lands.

[2] The gatehouse in Marygate and its lodge formed part of a range of buildings that linked to the older church of St Olave by a chapel dedicated to Mary.

Rebuilding began in 1270, under the direction of Abbot Simon de Warwick,[7] and was swiftly completed during a single twenty-four year building campaign,[4] such was the financial strength of the abbey.

[citation needed] In August 1513 the Abbot supplied four chests for the use of Philip Tilney, treasurer of the English army before the Battle of Flodden.

[13] A Vulgate Bible, sold at auction in England in 2010, has been identified as the possession of Brother John Grayson from St Mary's Abbey.

It includes the most detailed surviving description of a medieval parliament and a well-informed account of the Peasants' Revolt of 1381; these are likely to have been written by eyewitnesses and later incorporated into the chronicle.

[2] The relationship between the Museum and abbey is historically quite intimate as part of the richly carved chapter house vestibule (c. 1298–1307) survives incorporated into Tempest Anderson Hall lecture theatre (1911–12).

[18] Further excavations in the abbey were undertaken in 1952–56 by the then Keeper of the Yorkshire Museum, George Willmot who encountered the pre-Norman and Roman layers beneath the west wing of the nave.

[19] Excavations in 2014 and 2015 discovered an apse in the south transept, large parts of the wall foundations, and numerous residual small finds dating from the Roman to Modern periods.

One of the major conclusions of these excavations was the prevalence of in situ archaeological remains at a very shallow depth beneath the modern ground surface; in some cases as little as 7 cm underground.

Much stone was removed from the site in the 18th century, in 1705 for St. Olave's Church, between 1717 and 1720 for Beverley Minster, and in 1736 for the landing stage of Lendal Ferry.