He was also conscientious in ensuring that copies were made of his outgoing correspondence and other documents with a view to creating a body of evidence which could be used to prepare a historical account of the Covenanters.
He was licensed by Archbishop James Law and became a regent of Philosophy in the University, and tutor to the son of Alexander Montgomery, 6th Earl of Eglinton.
[4] Baillie accepted the liturgical changes introduced by James VI's Articles of Perth (1618), even elaborating an exhaustive defence of kneeling at communion in protracted correspondence with David Dickson, the minister for the parish of Irvine.
[5] His critical analysis of the intentions of its Canterburian authors is set out in his A parallel or briefe comparison of the liturgie with the masse-book, the breviarie, the ceremoniall, and other Romish rituals and Ladensium autakakrisis of 1641.
When, in 1662, he met Andrew Fairfoul, the recently consecrated Archbishop of Glasgow, he greeted him cordially, but made a point of not acknowledging his status.
A complete memoir and a full notice of his writings can be found in David Laing's edition of the Letters and Journals of Robert Baillie (1637–1662), Bannatyne Club, 3 vols.
Among his works are Ladensium αὐτοκατάκρισις, an answer to Lysimachus Nicanor by John Corbet in the form of an attack on Laud and his system, in reply to a publication which charged the Covenanters with Jesuitry; Anabaptism, the true Fountain of Independency, Brownisme, Antinomy, Familisme, etc., a sermon [in which he criticises the rise of the early Baptist churches in England such as those led by Thomas Lambe]; An Historical Vindication of the Government of the Church of Scotland; The Life of William (Laud) now Lord Archbishop of Canterbury Examined (London, 1643); A Parallel of the Liturgy with the Mass Book, the Breviary, the Ceremonial and other Romish Rituals (London, 1661).