Alexander Monro saw active service there for two and a half years, before returning to Scotland to complete his education.
Monro was tried by the Privy Council for refusing to pray for William III and Mary II in disobedience of the Act of Estates passed on 13 April 1689.
Although not ejected by the Privy Council he nevertheless resigned as Principal of the University of Edinburgh and from his charge in the north-eastern division of St Giles Cathedral on 24 April 1689.
On 20 September 1690 he was formally deprived of his Principalship by the Committee of Visitors (which had been appointed by Act of Parliament in July 1690 with wide-ranging powers while visiting Universities, Colleges and Schools).
Monro wrote a work in defence of his faith called An Enquiry into the New Opinions (chiefly) Propagated by the Presbyterians of Scotland; Together with some Animadversions on a Late Book entitled 'A defense of the Vindications of the Kirk'; in a Letter to a Friend at Edinburgh.
This prompted his successor as Principal of the University of Edinburgh, Gilbert Rule, to respond with a book called The Good Old Way Defended.