Following the resignation of Bishop John Gray on 4 March 1869, Archbishop Eyre was appointed the Apostolic Administrator of the Western District of Scotland on 16 April 1869. He travelled to Glasgow in March 1869, charged with organising the re-establishment of Roman Catholic hierarchy in Scotland. After attending the First Vatican Council (1869–70), he returned to Scotland in a mission to build schools and to unite the Scottish catholic community, bitterly divided between Scottish and Irish Catholics. In 1874, he opened St Peter's Seminary, Bearsden (subsequently removed to St Peter's Seminary, Cardross).