He was the eldest son of James Wishart of Cairnbeg in the parish of
Fordoun in
Aberdeenshire. His grandfather, James Wishart of Pittarrow had been clerk of the justiciary court and king's advocate. John succeeded his uncle, John Wishart, in the lands and barony of Pittarrow in 1545. Pittarrow is also often spelled "Pitarro". On 14 March 1557 he joined
Archibald Campbell, 4th Earl of Argyll,
Alexander Cunningham, 5th Earl of Glencairn, the
Lord James Stewart, and
John Erskine of Dun, in signing a letter to
John Knox, who was then at Geneva, inviting him to return to Scotland. During the next few years Wishart continued one of the leading members of the Protestant party in Scotland. On 24 May 1559 they met at Perth to organise resistance to the queen regent
Mary of Guise. Wishart and Erskine were chosen to assure her envoys that, while the
Lords of the Congregation had no disloyal intentions, but would firmly assert their privileges. On 4 June Wishart and Erskine had a conference at
St Andrews with Argyll and Lord James Stewart, who had been suspected of leanings towards the regent's party since the destruction of the monasteries. Soon afterwards Wishart and William Cunningham of Cunninghamhead were appointed to negotiate with Mary of Guise, on the subject of liberty of worship. A second deputation, of which Wishart was one, failed to obtain more than vague promises, and they proceeded to demand the banishment of her French supporters from the kingdom. Finding it impossible to gain satisfactory assurances from her, the protestant lords met at Edinburgh in October and elected a council of authority, to which Wishart was chosen. They drew up a manifesto in which it was declared that Mary of Guise had forfeited the office of Regent. In February 1560 he attended as commissioner the
convention of Berwick, where the
Duke of Norfolk, on behalf of
Queen Elizabeth, agreed to support the Lords of the Congregation with military force. In April the English army reached Edinburgh, and Wishart was prominent in welcoming it and promising co-operation. On 11 April he took part in a conference with the English envoys. Wishart was named one of the commissioners of burghs in the
Reformation parliament held at Edinburgh on 1 August 1560. and on 10 August he was chosen a temporal lord of the articles. This parliament ratified the confession of faith. The government of the state in the interval between the death of the queen regent and the arrival of
Mary, Queen of Scots was entrusted to a body of fourteen chosen from twenty-four persons nominated by parliament, of whom six, including Wishart, were selected by the nobility, and eight by Mary. On 24 January 1562 he was appointed a commissioner to value ecclesiastical property, with a view to compelling the clergy to surrender a third of their revenues for the support of the royal household. On 8 February 1562, he was knighted on the occasion of the marriage of the queen's brother
James Stewart, who was at that time
Earl of Mar, and
Annas Keith. On 1 March he was appointed
comptroller and collector-general of teinds, He became a member of the
privy council. where, however, he had sat as early as 6 December 1560. In this capacity he became paymaster of the reformed clergy, many of whom resented the scantiness of their stipends. According to Knox, the saying was current, "The good laird of Pittarro was ane earnest professour of Christ; but the mekle Devill receave the comptrollar". Wishart appointed a kinsman
George Wishart of Drymme as a sub-collector, and his account includes payments made by Mary to Knox and his servants. Wishart distinguished himself at the
battle of Corrichie, near Aberdeen, on 5 November 1562, by his services against the followers of the
Earl of Huntly. In the parliament held at Edinburgh on 5 June 1563 he was one of those appointed to determine who should be included in the act of oblivion for offences committed between 6 March 1558 and 1 September 1560.
John Knox told a story about the last words of
Lord John Stewart in 1563, a half-brother of Mary, Queen of Scots. Someone told her that Lord John's deathbed wish was that she would become a Protestant. Mary declared without hesitation that this was a lie invented by Wishart and her brother Moray's secretary
John Wood. Pitarrow and his wife Janet Falconer dined with the English diplomat
Thomas Randolph and the Earl of Moray on 27 February 1564. Pitarrow hoped Mary would marry "a good Christian" and "both the realms to live in friendship". When Mary made a progress to the north of Scotland in 1564, royal letters were carried between his house at Pitarrow and Edinburgh. ==Rebellion against Mary, Queen of Scots==