Thomas Prestbury clearly had very different relations with Richard II and was committed to the custody of the Abbot of Westminster in April 1399. He was elected Abbot of Shrewsbury in August, after the king had been imprisoned by Henry IV, which suggests he was suspected of Lancastrian sympathies. His efforts to mediate before the Battle of Shrewsbury in 1403 were in vain but he brought great prestige to the abbey as Chancellor of Oxford University. However, even he seems to have lived under the cloud of an accusation of felony.