He was granted the Chaplainry of Newmore to help pay or his university studies, in accordance with the plans of the reformer John Knox.
Subsequently he was presented to parish of Tain in 1599, and the charge of St Duthus Church in the burgh.
The Parish of Tain was one of the Presbyteries which opposed the proposed union, and in defiance of James' interdict, they sent John Munro as representative to an Assembly at Aberdeen on 2 July 1605; on that occasion he was nominated as Moderator.
[3] John Munro was to be sent to Kintyre, but in the meantime was imprisoned in Doune Castle, Perthshire,[1] with another of the ministers, Charles Ferm.
Following his flight from Edinburgh in 1607, Munro made his way to Tain and resumed his ministry among the people there, though without the stipend previously paid by the Crown.
On 24 May 1610, the Scottish Privy Council sent a letter to the Provost and Bailies of Tain, admonishing them for permitting the Munro to remain living among them and to continue preaching unmolested.