Upon taking office the following year, Flaget found himself charged with the pastoral care of the western frontier of the United States, having the assistance of seven priests. In 1814, there being no Anglican clergyman in St. Louis, George Rogers Clark asked his old friend, Flaget, to baptize his three oldest children. Flaget went on to build St. Joseph Cathedral in Bardstown as the center of the diocese and a seminary to train the clergy needed to carry out the work of the diocese. He was one of only two bishops of Bardstown (along with John Baptist Mary David), though, since the diocese was removed to Louisville, Bardstown remained a titular see.