On 11 February 1636 he was preferred to the see of Dunblane, in succession to Adam Bellenden, promoted to the bishopric of Aberdeen. He must have retained the prebend of Whitchurch, as no successor was appointed until 1 July 1638. When the Glasgow assembly of 13 December 1638 deposed the bishops, Wedderburn was expressly included in the excommunication, because "he had been a confidential agent of Laud, archbishop of Canterbury, in introducing the new liturgy and popish ceremonies". (See Bishops' Wars and National Covenant for context.)