During Edward II's reign, the king formed close attachments to a few favourites. This immediately alienated the English nobility, some of whom rebelled against the king in order to assert their rights in the government. Edward's humiliating defeat in Scotland against Robert Bruce's forces and the resulting truce with the Scottish spurred Queen Isabella into action against the weak king. In 1325, Isabella was sent to the court of her brother, King Charles IV of France, in order to negotiate a dispute between England and France. Whilst in France, Isabella obtained assistance from Count William of Hainault to invade England and overthrow Edward II. In September 1326, Isabella, along with Hainaulter mercenaries, arrived in England. Those nobles who had been alienated by Edward's favouritism supported Isabella plan to seize the throne for her son. By early 1327, Edward II had been deposed and executed. The continuing conflict with the Scottish led Isabella to maintain her alliance with the Hainaulter mercenaries, which was formalised in the marriage between Edward III and Phillipa of Hainault.
In 1243, the Franciscans, or Friars Minor built a friary south of the castle. The friary lay between the city wall and the street called Friargate. The site ran south towards the Ouse, and about 1290, the friars built a wall along the riverbank.
The friary was used as a royal lodge because of its proximity to the castle; Edward II, Edward III and Richard II stayed there when visiting York. In 1327, the English court stopped in York to break their journey north towards Newcastle. The young king Edward III and his mother Isabella lodged at the friary. They were joined by Sir John de Hainault, an ally the campaign against the Scottish. As the nobility feasted on the night of 7 June, the servants of the Hainaulters and the English archers billeted with them quarrelled over a game of dice. This quarrel escalated into a riot as the Hainaulters and the Lincolnshire archers armed themselves, resulting in several hundred dead. Some of the dead may have been buried in a mass grave at St. Clements Nunnery, which would have stood between the river Ouse and Bishopgate Street.