During the progress of the Sarah Hewley suit, Wilson's judgment went entirely with the defendants, and his religious views, probably under Hunter's influence, underwent a change in the Unitarian direction.
He published an instalment of The History and Antiquities of Dissenting Churches and Meeting Houses in London, Westminster, and Southwark: including the Lives of their Ministers in 1808, 2 vols.
A third volume of his Dissenting Churches appeared in 1810; a fourth in 1814, with a preface (1 May 1814) showing his personal interest in the older types of nonconformity.
According to Alexander Gordon in the Dictionary of National Biography, the later volumes of his work exhibit a softer attitude towards the free-thinkers of dissent, and his facts are given fairly.
[2] Wilson attributed 210 works to Defoe, in some cases loosely or with caveats, adding about 80 items to the list given by George Chalmers.
He bequeathed his manuscript collections for the history of dissent to Dr. Williams's Library; a list of these, by the then librarian, Richard Cogan, was printed in the Christian Reformer (1847, p. 758).