He took an active interest in the affairs of the Irish Church, and was for many years a member of the general synod and representative church body.
This last work is an exhaustive study of the foreign relations of the early Irish Church, especially its relations with Rome and its missionary work.
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In the history of the Irish church Trench chiefly deserves to be remembered for his activity in promoting the remarkable evangelical movement in the west of Ireland which was known in Connaught as the Second Reformation, and which, chiefly through the agency of the Irish Society, made a vigorous effort to win converts to Protestantism.
When, in the aftermath of the crisis over Henry VIII's marriage to Catherine of Aragon, the Irish Church was ordered to formally break its link with the Roman Catholic Church to become the Church of Ireland, the Anglican or Church of Ireland Bishop of Meath continued to live in Ardbraccan in an estate attached to the main church.
As Secretary he engaged in a correspondence on Church of Ireland proselytizing which was published as Proselytism in Ireland: the Catholic Defence Association versus the Irish Church Missions on the charge of bribery and intimidation; a correspondence between the Rev. Alex Dallas and the Rev. Henry Wilberforce (1852).
The Synod of Kells in 1152 restructured Catholicism on Ireland, replacing a monastic system of directing the Irish Church with a system of parishes, dioceses and archdioceses.