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.
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.
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.
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.
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".
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.
He was denounced as a rebel, and compelled to fly to England, where he remained until the assassination of David Rizzio on 9 March 1566 and the alienation of Mary from Darnley enabled him to return.
On 19 November he was appointed an extraordinary lord of session, and in October 1568 accompanied the regent Moray to York to support his charges against Mary.
[22] As Laird of Pitarrow, he is sometimes confused with Henry Echlin of Pittadro, who was at this time the Constable of Edinburgh Castle with William Kirkcaldy of Grange.
The English ambassador Thomas Randolph had a very high opinion of Wishart, and described him as "a man mervileus wyse, discryte, and godly, withowte spotte or wryncle.