In 1453, John Bonally, the Prior of Urquhart formally requested from the Pope that his monastery and Pluscarden be merged. At that time, Urquhart had only two monks and Pluscarden had six. A Papal Bull was issued by Nicholas V on 12 March 1453 joining the priories and from then on Pluscarden became a daughter house of the Benedictine Dunfermline Abbey. Pluscarden was chosen over Urquhart for the priory location as the buildings were more spacious and thought easier to restore and Bonally was appointed as its first Benedictine prior. However, the Abbot of Dunfermline's representative informed him that he found the priory in need of much renovation; the consequence of nearly 60 years of neglect was that vaulted roofs of the choir and crossing were in danger of collapsing. About the time of John Bonally irregularities had become commonplace in the Priory of Pluscarden as well as before that at Urquhart and the priors of both places were accused of much sinfulness. Following a commission held into the alleged abuses, Bonally resigned and was succeeded by William Boyce who was the sacrist at Dunfermline Abbey. William Boyce, the second Benedictine Prior of Pluscarden, was given responsibility for the maintenance of the church fabric of Dunfermline Abbey from Abbot Richard de Bothwell (1445–70) at the time that the west end of the abbey's nave was restored. The inference has been made that it was during this prior's tenure that some major improvements were carried out at Pluscarden. Indeed, by 1506, King James IV was able to stay at the priory and was noted as giving the masons working on the building a sum of 15 shillings for buying drink.