Fasting, almsgiving, and the visitation of the sick were among the main objects of the friends, and the influence of Clayton's devotional spirit and earnest churchmanship was felt in the little community.
Clayton acted as chaplain to Darcy Lever, LL.D., high sheriff of Lancashire in 1736, and published the assize sermon which he preached at Lancaster in that year.
His high-church practices and strongly pronounced Jacobite views proved very obnoxious to the Whig party of the neighbourhood.
He was attacked in a pamphlet by Thomas Percival of Royton, and subsequently by Josiah Owen, presbyterian minister of Rochdale, and John Collier, otherwise known as 'Tim Bobbin'.
When the Young Pretender visited Manchester in 1745, Clayton publicly advocated his claims, and offered up prayer in the collegiate church for the deposed royal family.
Afterwards Clayton had to suffer: he was obliged to conceal himself, and was suspended from his office for violating his ordination vow, and for acting as one disaffected towards the Protestant succession.
For many years Clayton ran an academy at Salford, and his pupils after his death formed themselves into a society called the Cyprianites, and at their first meeting decided to erect a monument to his memory in Manchester Cathedral.