The Black Death had, of course, a devastating impact on Malmesbury Abbey, just as it did on every community in England. Victims probably included Abbot John of Tintern, and the prior of the dependent cell at Pilton, John of Lokyngham, both of whom died in 1349. There were doubtless many other victims in the monastery and the neighbourhood of the Abbey. There is no documentary evidence relating specifically to the death rate among the monks of Malmesbury Abbey but data from other Benedictine communities suggests that the mortality level was often extremely high. At Durham Cathedral Priory about half of the community died during the Black Death. Although we do not know how many monks died, it is possible to estimate quite precisely the rate of mortality among some of the rural poor in the Malmesbury area using the records of Glastonbury Abbey which owned property extremely close to Malmesbury Abbey in north Wiltshire. Four Glastonbury manors lay within a ten-mile radius of Malmesbury: Christian Malford, Grittleton, Kington and Nettleton. The village of Christian Malford was just six miles from Malmesbury and immediately adjacent to the manor of Sutton Benger which belonged to Malmesbury Abbey. Records survive from the Glastonbury archive which can be used to demonstrate the death rate of ‘garciones’, adult male villeins without land, on Glastonbury's Wiltshire estates. It is reasonable to assume that the mortality rate in the villages owned by Malmesbury Abbey resembled that on the nearby Glastonbury lands, where the death rate among this class of villeins ranged from 48% to 66%.

The mortality for townsfolk was doubtless high also. One indicator of the disappearance of whole households in the town is found in legal records from 1352, which state that four men from Malmesbury – Nicholas Handsex, Thomas Smyth, Richard Uphulle and Thomas Terry – were guilty of ‘carrying doors and windows from empty tenements in Malmesbury’.

At a national level the shortage of labour after the Black Death created problems for monastic landlords, and eventually led to the end of direct demesne farming. At Malmesbury this process was protracted: the abandonment of demesne farming took place at some point in the early fifteenth century. The ‘inquisition post-mortem’ for Abbot Walter of Camme, following his death in 1396, indicates that his demesnes were largely still in hand, although with dilapidated buildings and lands wasted by the pestilence.