From 1949 until 1988, the seminary was under the jurisdiction of the bishop of the St. Cloud Diocese. See the Summer 1988 SJU Alumni Magazine article (p. 11):
“In conjunction with the appointment of a new Rector, Bishop Hanus and Abbot Jerome announced revision of the 1949 agreement between the Diocese of St. Cloud and Saint John’s Abbey concerning the seminary. For 38 years the diocese has owned and managed the seminary building and provided personnel for the seminary program. Under the new arrangement the diocese will continue to assist in staffing the seminary, but will transfer ownership of St. Cloud Hall [now Emmaus Hall], the seminary building, to Saint John’s. The seminary program will continue under the auspices of the Abbey and the University.”