Having been licensed as a preacher of the gospel, he was presented by the Duke of Montrose to the church of Killearn, the parish adjoining his father's.
In the General Assembly and Presbytery, and from his pulpit, he defended the church's spiritual freedom against "ecclesiastical tyranny".
When the General Assembly of the Church of Scotland in 1752 deposed Thomas Gillespie of Carnock, Baine pleaded for him.
In the end he joined Gillespie, the founder of the Relief Church, resigning his living of Paisley on 10 February 1766.
He published, on his deposition, 'Memoirs of Modern Church Reformation, or the History of the General Assembly, 1766, with a Brief Account and Vindication of the Presbytery of Relief.'
Prior to his deposition and induction — the latter of which was conducted by Thomas Gillespie, of Carnock and Dunfermline — a tradition runs that he and his people worshipped in Old Greyfriars under the venerable Dr. John Erskine, and sat down together at the sacrament of the Lord's Supper there.
In 1777 he published a volume of sermons of fairly representative character, though, as is frequently the case, it is very evident that they needed his eye and voice to interpret them.