He was Minister of St Andrew's Church from 1836 to 1883, and was the first Moderator of the General Assembly of the Presbyterian Church in Canada in June 1875. He had also served as Moderator of the Church of Scotland's Canada Synod in 1838, not long after his arrival. Despite being under the tutelage of Free Church leader Professor Thomas Chalmers at Edinburgh, Cook remained with the Established Church in June 1844. He was asked to moderate the remainder of that Synod meeting in Kingston, following the defection of Moderator Mark Young Stark.
In June 1975, Canada Post honoured the Centenary of the Presbyterian Church in Canada with the issue of a postage stamp in honour of Cook. He was awarded the Doctor of Divinity in 1838 from the University of Glasgow, and the LLD from Queen's in 1880, following his term as Chancellor.