In 1563 John Durie was Exhorter in Parton, Galloway, later exhorter at Colinton and Restalrig (1567-69) then Minister in Penicuik, near Edinburgh (1570), then Minister in Restalrig again (1570-72), then minister at St Giles, Edinburgh, the primary church of Scotland (1574-79). Chalmers History of Dunfermline (vol. i. p. 307, &c.) records that in 1574 “Mr. John Durie, the learned Monk of Dunfermline," but now an eminent preacher of the Protestant faith, “this year began his active crusade against the bishops”.

In 1575 John was imprisoned with Walter Balcanqual in Edinburgh Castle for being critical of the Scottish court. In 1582 (23 May) John was ordered to leave Edinburgh (on internal exile) but got leave to return and on 4 September the people of Edinburgh met him at Leith and marched him up the High Street singing the 124th psalm, in imitation of Christ's return to Jerusalem. We have to assume he was not without influence in the city, as he had married Marion Marjoribanks, daughter of Edinburgh's Lord Provost.

In 1590 John Durie received an annual pension of 140 shillings Scots from the King. John, with Archie Stewart, was the last man to see John Knox alive (17 November; he died on 24 November).

John Durie seems to have spent out his last years in Montrose comfortably and happily. He lived to see two of his sons, Joshua and Robert, follow in his footsteps into the ministry, and to watch Simeon and three young daughters grow up: Joshua became minister of Inverkeillor; Robert, Minister of Anstruther (but with many other adventures and eventually the founding of the Scots Kirk in Leyden, Holland); Simeon had the ministry of Arbroath; Christian married George Gledstanes, Archbishop of St Andrews; Elizabeth married James Melville, minister of Kilrenny; and an unnamed daughter married John Dykes, also minister of Kilrenny). His grandson, also John Durie, became a Protestant crusader throughout Europe.

John Durie died on 28 February 1600, by all accounts in great peace of mind. He had also been a good athlete.