In Edinburgh (1561-1571) John Craig became minister of the
Canongate in 1561, making him
Mary, Queen of Scots's royal chaplain at
Holyrood House in Edinburgh. In April 1562,
John Knox requested that Craig might become his colleague in
St Giles' Cathedral, and this was carried out, according to the Fasti, in 1563. The council wrote: "The Council understanding the tedious and heavy labours sustained by their minister, John Knox, in preaching thrice in the week, and twice on the Sunday, ordains unanimously to solicit and persuade Master John Craig, presently minister of the Canongate, to accept upon him the half charge of the preaching in the said Kirk of Edinburgh, for such good deed as they can agree upon." There seems to have been a problem with Craig's salary but Kerr asserts: "Stipend problems apart, it is quite clear...that Craig was one of the ministers of St. Giles’ as from the summer of 1562." Knox and Craig seem to have supported one another's ministries. Kerr says: "It was through Craig being at St. Gile's that Knox had greater freedom of movement to prosecute his missionary work than he otherwise would have had." The pastoral work was divided in two and both preachers undertook tours to strengthen their cause in other parts of the country: Knox in Nithsdale, Galloway and Kyle in autumn 1562, and Craig in Jedburgh the following year. They were later able to leave Edinburgh simultaneously for example in 1564 when Craig went back to the Merse churches for a month while Knox engaged in similar work north of the Forth. The two men supported each other in public life too. Knox was pleased by Craig's outspokeness against the nobility and called him "that worthy servant of God", approving is his public rebuke of courtiers. Craig supported Knox in the General Assembly too. In the debate about church and state relations, around the topic of the Queen's Mass, as Knox argued for denying the queen the Mass, with Craig providing supporting arguments on resisting rulers, whereas
John Winram and
John Douglas would have allowed her to celebrate it. Craig presented a personal petition to the General Assembly of June, 1566. He desired that "John Cairns who had read prayers and exhorted four years and more in Edinburgh, and had well profited, might be joined with him in the Kirk of Edinburgh, in respect he was alone." The Assembly ordered the church of Edinburgh, with the assistance of
John Spottiswood, to consider the matter. Apparently the crave was not granted for, Cairns's name appears in Town Council Minutes for many years afterwards as simply that of "reader". He is first mentioned in these Minutes as minister (and so thereafter) on 13 November 1584, and in that of 15 July 1586, as "ane of the ordinar ministers of this burgh . . This independent action on Craig's part, might be construed as being disloyal to Knox still absent from Edinburgh but, at this time, Craig, besides his General Assembly work, was in sole charge at St. Giles’ and urgently in need of ordained assistance.
In Montrose (1571-1573) In 1571 he was sent by the assembly to Montrose "for the illuminating the north, and when he had remained two years thence to Aberdeen to illuminate those dark places in Mar, Buchan, and Aberdeen, and to teach the youth of the college there."
John Durie, who was also a minister at St Giles, followed Craig as minister of Montrose.
In Aberdeen (1573-1579) Craig moved to Aberdeen on 6 August 1573, where he remained six years, where he was named Superintendent of Mar and Buchan. It was at Aberdeen that Craig wrote and used his
A Shorte Summe of the Whole Catechisme. At Aberdeen Craig passed six years of incessant activity. He was appointed commissioner for visiting the province of Aberdeen in 1575, and was employed in similar functions in 1576 and 1578. He was member of twelve out of thirteen Assemblies, and in that of October 1576 he was elected moderator for a second time. It was during this period that the controversy was carried on concerning the lawfulness of the episcopal office. The question was debated in August 1575 by a committee appointed for the purpose, in which Craig, with
Andrew Melville and James Lawson, was to take the negative side. Their report in condemnation of the order was approved in all points in the following year, and in 1581 bishops were utterly abolished. Craig had also a hand in the drawing up of the Second Book of Discipline, which was agreed upon in the Assembly of 1578. It was during his ministry here that he prepared his first or longer Catechism, as in the preface to the work he reminds "the Professovres of Christis Evangell at Newe Abirdene" that it was for their sake chiefly that he "toke paines first to gather this breife summe" and he now (July 1581) in setting it out and making it common to others, recommends the same to them again in special as a token of his goodwill, and a memorial of his doctrine and earnest labours bestowed upon them for the space of six years. In the fortieth Assembly, held at Edinburgh, 7 July 1579 among certain Articles presented to the king was a petition that, as "his Highness' house is too great a charge for any one man, his Majesty would be pleased to nominate any one of the best-gifted in the kingdom to be adjoined colleague to
Mr, John Duncanson" and in the following year, 12 July, it appears that "the king by his letters nominates Mr. John Craig to be his minister, for which the Assembly blessed the Lord, and praised the king for his zeal". Meanwhile, in view of his appointment as Royal Chaplain, Craig had left Aberdeen, 14 September 1579, with his wife and family.
In Edinburgh (officially the Chapel Royal of Stirling 1579-1600) Craig left Aberdeen on 14 September 1579, to undertake the charge of minister of the
Chapel Royal of Stirling. This meant he became domestic chaplain to
James VI. A chamber was prepared for him in
Holyrood Palace by the
master of work William MacDowall at a cost of £25-8s-1d. In January 1581 he criticised
James Stewart, Earl of Arran by preaching on the subject of false accusations. Arran had accused
Regent Morton of involvement in the murder of
Lord Darnley, and he threatened Craig with a dagger. King James had personally appointed Craig, "one of the best-gifted in the kingdom" as his Royal Chaplain, so when Craig rebuked him during his
captivity so sharply from the pulpit (19 September 1582) for having issued a proclamation offensive to the clergy, "the king wept". ==Craig's views on church-state relations==