In the wake of the Revolution, the General Assembly of 1690 restored Williamson to the West Kirk. In line with his earlier prophecy, Williamson ministered in the charge until the day of his death. Williamson served as one of the commissioners sent by the Church of Scotland to congratulate William II on his accession. Williamson was elected to the General Assembly of 1692 and served as the Assembly's moderator in 1702. In later life, Williamson invested £100 in the Darien scheme. He died "without painful sickness, generally esteemed" on 6 August 1706 at the age of around 72. He bequeathed a manse to his successors.