Abbot William of Badminton (1296–1324) had a long and distinguished public career, and David Knowles considered that he was ‘the only abbot of note’ produced by Malmesbury after 1216. Towards the end of his abbacy he became entangled in the bitter conflict that broke out between Edward II's advisers, the Despensers, and the king's baronial opponents; but prior to this he had been a successful and respected prelate. In 1298, soon after becoming abbot, Badminton was chosen as one of the ‘presidents’ who organised the provincial chapter or conference of all Benedictine abbots in those parts of southern England subject to the archbishop of Canterbury. He continued to act as president until 1310 or 1311, visiting Rome twice, in around 1301–2 and also at some point between 1309 and 1314. Badminton played a central role in the campaign to ensure that the most talented Benedictine monks from English monasteries received a university education. In 1283 a small dependent cell of monks from Gloucester was established at Oxford, and in the 1290s the provincial chapter decided to expand Gloucester College, as it was known, and to make it a college for Benedictine monks from all over the Canterbury archdiocese. In 1298 Malmesbury Abbey was given a major stake in the governance of the institution. By this time a pious nobleman, Sir John Gifford, who owned the college's site, was living in retirement at Malmesbury Abbey, and he granted formal ownership of the premises to Malmesbury: the abbots of Malmesbury became the landlords of the college. William of Badminton appointed the first prior of the newly constituted college, and Malmesbury monks remained involved in the management of the institution throughout the fourteenth century. The site of the college is today part of Worcester College, and a late medieval sculptural shield bearing a griffin, the heraldic device of Malmesbury Abbey, can still be seen on the doorway of one set of rooms.

There is no reason to doubt that the Divine Office was taken seriously under the rule of William of Badminton. A beautiful psalter and hymnal survives from early fourteenth-century Malmesbury, which is held today in the library of Sankt Gallen in Switzerland. The manuscript contains a calendar of feasts celebrated by the Malmesbury monks and the text of the version of the Litany of Saints used by the Abbey.