It provoked a reply from James Small, an Episcopalian, which was answered by Willison in his Letter from a Parochial Bishop to a Prelatical Gentleman.
After the ejection of Ebenezer Erskine and his fellow-ministers for opposition to patronage, Willison attacked their exclusion in a sermon to the Synod of Angus and Mearns in 1733 (published as "The Church's Danger").
Erskine and his colleagues were not satisfied and formed a separate presbytery in 1739 (see United Presbyterian Church of Scotland for Seceders history).
In 1737 he wrote one of his most famous and most reprinted works The Afflicted Man's Companion, and also an explanation of the Shorter Catechism called An Example of Plain Catechising.
During the Jacobite rebellion of 1745, having published in the same year Popery Another Gospel, he was threatened by soldiers of the Highland army while conducting service in the church building and for a few weeks had to preach in private houses.