His failure to convince King William III and II that the Scottish bishops could be trusted led to the abolition of Episcopacy in Scotland.
Rose continued as a nonjuring bishop, eventually becoming leader of the informal and embryonic Scottish Episcopal Church.
He was ordained as "second Charge" minister of St John's Church in Perth in August 1672, but only after the town had unsuccessfully tried to secure the appointment of Alexander's uncle, Arthur Rose.
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.
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 continued to act as a nonjuring bishop, privately acknowledging the primacy of his uncle, now Archbishop of St Andrews.
Routinely suspected of Jacobitism, under severe pressure, and suffering declining number of sympathising ministers, Rose quietly led as the metropolitan of Scottish Episcopalians.
Their son John Rose fought in the Jacobite Rebellion of 1715, and was captured at the battle of Sheriffmuir, though he obtained clemency partly due to his father's influence.