Returning to Scotland as the chaplain of James, Marquess of Hamilton, he was given charge of the churches of Harray and Birsay on 27 June 1641.
Aitken remained a staunch royalist during the English Civil War, and after the failure in 1650 of the campaign of James Graham, 1st Marquess of Montrose, fled to the Netherlands.
He returned to Scotland during the Cromwellian Protectorate and resided in Edinburgh for most of the period between 1653 and 1660, moving his family from Orkney.
With the Restoration of the latter year and the return of the monarchy, Aitken's known loyalty to the crown was rewarded with patronage.
As Bishop of Galloway, he received permission to reside in Edinburgh because, in the words of Robert Keith, "it was thought unreasonable to oblige a reverend prelate of his years to live among such a rebellious and turbulent people"[2] He died on 15 November 1687, and was buried in Greyfriars Church, Edinburgh.