Rose's career rise continued. In December of this year, he was recommended by the king to be selected as the new Bishop of Moray. The royal mandate for his consecration was issued on 8 March 1687. However, before even taking possession of the diocese of Moray, he was translated to the diocese of Edinburgh, after his name had been put forward by Colin Lindsay, 3rd Earl of Balcarres. He was elected on 21 December, and despite the protests of some dissenting ministers, was appointed to the position on 31 December. In December 1688, Bishop Rose and Bishop Andrew Bruce were chosen by the Scottish bishops to travel to London, but Bishop Bruce fell ill and Rose was compelled to continue alone. The situation he found himself in was having to decide on behalf of all the Scottish bishops whether to support William of Orange or James VII and II. William was prepared to retain Episcopacy in Scotland if the bishops would acknowledge him. Probably on 30 January 1689, Bishop Rose met with King William. Bishop Rose was sympathetic to King James, and though William's cause had already clearly triumphed, he was not sure about committing the other Scottish bishops. When asked for his support, Bishop Rose gave a highly ambiguous reply:
Sir, I will serve you as far as law, reason, or conscience shall allow me.
Rose returned to Scotland without having committed either the bishops to King William, nor King William to the bishops. Later in the year, Rose was almost certainly one of the seven Scottish bishops who voted against renouncing their oaths to King James and offering the Scottish crown to William. This was probably enough to convince King William that the Scottish bishops were too sympathetic to Jacobitism, and there were more than enough hard-line Presbyterians in Scotland who hated the existence of bishops. It was thus that, on 20 July 1689, Episcopacy in Scotland was declared abolished and all bishops were deprived of their sees within the Church of Scotland.
Rose continued to act as a nonjuring bishop, privately acknowledging the primacy of his uncle, now Archbishop of St Andrews. Though deprived of any formal authority, Rose gained informal influence over the embryonic Scottish Episcopal Church. After the death of Arthur Rose in 1704 and then John Paterson in 1708, Archbishop of Glasgow, Alexander Rose was regarded as the senior nonjuring bishop in Scotland. In 1705, along with Bishop Douglas of Dunblane, he performed the consecration of John Fullarton and John Sage. He consecrated five more bishops between 1709 and 1718. Routinely suspected of Jacobitism, under severe pressure, and suffering declining number of sympathising ministers, Rose quietly led as the metropolitan of Scottish Episcopalians. He also tried to obtain the help of Church of England and Queen Anne. He was involved in the Jacobite rising of 1715, as a trustee of the "Old Pretender", James Francis Edward Stuart.