As John J. Conroy had been appointed to St. Joseph's Church in Albany, Bishop Hughes appointed Bayley to replace him as vice-president of St. John's College, where he also served as professor of rhetoric and "belles-lettres". He began his duties on April 1, and at the same time assumed responsibility for missionary stations in New Rochelle and Port Chester, each of which he visited once a month. In the following school year, he took on the additional duties of acting as prefect of discipline for the seminarians and of lecturing on Holy Scripture.