In 1798 he issued a sentence of excommunication against all those of his flock who would join the rebellion. In a pastoral read in all the churches, he spoke of the clerical organisers of the rebellion as ‘vile prevaricators and apostates from religion, loyalty, honour, and decorum, degrading their sacred character, and the most criminal and detestable of rebellious and seditious culprits.’ Troy's action at this time appears to have endangered his life; but the influence he had acquired with the government enabled him to moderate the repressive measures taken by the authorities. Believing that Catholic emancipation could never be conceded by the Irish parliament, he was one of the most determined supporters of the Union.