The succession crisis that followed the death of Henry I in 1135 led to protracted political turmoil and conflict in England. Civil war broke out in 1139, and the monks of Malmesbury witnessed several episodes of conflict in the years that followed. We are blessed with exceptional sources for the study of Malmesbury during Stephen's turbulent reign. William of Malmesbury provided commentary on the early stages of the conflict between Stephen and Matilda in his Historia Novella. William was not an objective witness because the work was commissioned by Robert of Gloucester, Matilda's half-brother and general, who was one of the main actors in the events of the period. Despite his partisan perspective the Historia Novella was carefully written and well-informed, and it remains a source of immense value to historians today. William’s testimony breaks off towards the end of 1142 but the anonymous chronicle, the Gesta Stephani, provides a narrative guide to the whole conflict. Gesta Stephani was written by someone with in-depth knowledge of the Malmesbury area: over a quarter of all the places mentioned in it lie within a 25-mile radius of Malmesbury. On the basis of substantial circumstantial evidence the author has been identified as Robert of Lewes, Bishop of Bath. In addition to the Historia Novella and the Gesta Stephani, other chroniclers such as Henry of Huntingdon and John of Worcester provided detailed accounts of events at Malmesbury during the Anarchy.

It is clear from these contemporary sources that both sides in the war between Stephen and Matilda were anxious to control Malmesbury because of the strategic importance of its castle. The precise location of the castle is not known but it was undoubtedly very close to the conventual church. In his Historia Novella William of Malmesbury stated that Bishop Roger had established the castle ‘in the churchyard itself, hardly a stone’s throw from the abbey’. No trace remains above ground of the structure because the monks, who greatly resented the castle's existence, completely destroyed all traces of the fabric following their acquisition of the site in 1216. However, we can surmise that the castle was substantial and built to a high specification because it was besieged in 1144 and 1153 but on both occasions the attackers were unable to take it by force.