The division occurred because of a continuing difference over liberty of conscience (as defined in the Westminster Confession of Faith), which came to a head over the attendance of Lord Mackay of Clashfern at a Requiem Mass which formed part of the funeral of a colleague, former Lord Justice Clerk Lord Wheatley. As Mackay was Lord Advocate for Scotland, it was expected that he attend the funeral of a deceased member of the judiciary; Wheatley was also a friend of Mackay. However, Mackay was also an elder in the Free Presbyterian Church, and its leadership found his attendance intolerable, as it regards Roman Catholicism as spurious and the Mass as idolatrous. As a result, Mackay was suspended from office. Some in the church disagreed with this punishment and a split ensued, not only over the Mackay affair but also the ongoing issue of freedom of conscience. The people who formed the APC believed that liberty of conscience was not being given sufficient place in the Free Presbyterian Church, and that the disciplinary action taken by the Free Presbyterian authorities against Lord Mackay was inappropriate.
The Associated Churches website states: "We believe that it is correct to allow Christians to make their own decisions on matters that are not fundamental to the faith."
The church's beliefs "are stated in a confession that is catholic, Reformed, and biblical, and which states the historic convictions of the Church of Scotland" the Westminster Confession of Faith.