Winram played a leading role in the early organisation of the newly independent Scottish Church, maintaining a high work-load as an administrator into his 80s.

The former suffered from severe disability, though the latter was healthy and he and Winram had a mutually beneficial relationship until the death of Margaret led to a dispute about her will.

[2] At the trial of George Wishart in 1546 Winram preached the opening sermon, the subject being "Heresy," which he very safely defined as "a false opinion defended with pertinacitie, cleirlye repugning to the word of God" (summary in Knox[3] and in Lindsay of Pitscottie's Chronicle, pp. 459–60).

That Wishart believed the sub-prior to be favourably disposed towards him may be inferred from the fact that while waiting in the castle of St. Andrews before execution it was for him he sent in order to make his confession.

[5] Winram was present at the meeting of the provincial council held in Edinburgh in November 1549, at which special resolutions were passed for reforming the lives of the clergy (Robertson, Stat.

82–4); and by some he is supposed to have been the author of the catechism, known generally as Archbishop Hamilton's, approved by a provincial council held at Edinburgh in January 1552.

[2] Although present at the trial of Walter Milne in 1558 and at a provincial council held in 1559, Winram cast in his lot with the reformers as soon as their cause seemed likely to prevail; and, being nominated by the lords superintendent of Fife, 9 July 1560, he was admitted at St. Andrews 13 April 1561.

[6] He was present at the parliament at which it was ratified, and spoke in its support (Randolph to Cecil, 19 Aug.),[7] and, after the ratification, was appointed one of a commission to draw up the "Book of Discipline".

At nearly every general assembly from 1562 to 1570 complaint was made against him as superintendent for slackness in visitation and preaching; and his "immersion in worldly affairs" also gave offence to the more censorious.

He also attended the convention held at Leith in January 1572, at which the creation of the 'tulchan' bishops was authorised; and under the new arrangement he was made archdeacon of the diocese, resigning the superintendentship of Fife to the new archbishop, and being designated instead superintendent of Strathearn.